Promoter, promoter control elements, and combinations, and uses thereof

ABSTRACT

The present invention is directed to promoter sequences and promoter control elements, polynucleotide constructs comprising the promoters and control elements, and methods of identifying the promoters, control elements, or fragments thereof. The invention further relates to the use of the present promoters or promoter control elements to modulate transcript levels.

CROSS REFERENCES TO RELATED APPLICATIONS

This application is a Continuation of co-pending application Ser. No.11/598,118, filed on Nov. 10, 2009 the entire contents of which arehereby incorporated by reference and for which priority is claimed under35 U.S.C. §120.

The nonprovisional application Ser. No. 11/598,118, filed on Nov. 10,2006, claims priority under 35 U.S.C. §119(e) on U.S. application Ser.No. 10/950,321, filed Sep. 23, 2004, and Provisional Application No.60/505,689 filed on Sep. 23, 2003; Application No. 60/511,460 filed onOct. 14, 2003; Application No. 60/518,075 filed on Nov. 6, 2003;Application No. 60/527,611 filed on Dec. 4, 2003; Application No.60,529,352 filed on Dec. 12, 2003; and Application No. 60/544,771 filedon Feb. 13, 2004, the entire contents of each of which are hereinincorporated by reference.

FIELD OF THE INVENTION

The present invention relates to promoters and promoter control elementsthat are useful for modulating transcription of a desiredpolynucleotide. Such promoters and promoter control elements can beincluded in polynucleotide constructs, expression cassettes, vectors, orinserted into the chromosome or as an exogenous element, to modulate invivo and in vitro transcription of a polynucleotide. Host cells,including plant cells, and organisms, such as regenerated plantstherefrom, with desired traits or characteristics using polynucleotidescomprising the promoters and promoter control elements of the presentinvention are also a part of the invention.

BACKGROUND OF THE INVENTION

This invention relates to the field of biotechnology and, in particular,to specific promoter sequences and promoter control element sequenceswhich are useful for the transcription of polynucleotides in a host cellor transformed host organism.

One of the primary goals of biotechnology is to obtain organisms, suchas plants, mammals, yeast, and prokaryotes having particular desiredcharacteristics or traits. Examples of these characteristic or traitsabound and may include, for example, in plants, virus resistance, insectresistance, herbicide resistance, enhanced stability or additionalnutritional value. Recent advances in genetic engineering have enabledresearchers in the field to incorporate polynucleotide sequences intohost cells to obtain the desired qualities in the organism of choice.This technology permits one or more polynucleotides from a sourcedifferent than the organism of choice to be transcribed by the organismof choice. If desired, the transcription and/or translation of these newpolynucleotides can be modulated in the organism to exhibit a desiredcharacteristic or trait. Alternatively, new patterns of transcriptionand/or translation of polynucleotides endogenous to the organism can beproduced. Both approaches can be used at the same time.

SUMMARY OF THE INVENTION

The present invention is directed to isolated polynucleotide sequencesthat comprise promoters and promoter control elements from plants,especially Arabidopsis thaliana, Glycine max, Oryza sativa, and Zeamays, and other promoters and promoter control elements functional inplants.

It is an object of the present invention to provide isolatedpolynucleotides that are promoter sequences. These promoter sequencescomprise, for example,

-   -   (1) a polynucleotide having a nucleotide sequence as set forth        in Table 1, in the section entitled “The predicted promoter        sequence” or fragment thereof;    -   (2) a polynucleotide having a nucleotide sequence having at        least 80% sequence identity to a sequence as set forth in Table        1, in the section entitled “The predicted promoter sequence” or        fragment thereof; and    -   (3) a polynucleotide having a nucleotide sequence which        hybridizes to a sequence as set forth in Table 1, in the section        entitled “The predicted promoter sequence” under a condition        establishing a Tm−20° C.

It is another object of the present invention to provide isolatedpolynucleotides that are promoter control element sequences. Thesepromoter control element sequences comprise, for example,

-   -   (1) a polynucleotide having a nucleotide sequence as set forth        in Table 1, in the section entitled “The predicted promoter        sequence” or fragment thereof;    -   (2) a polynucleotide having a nucleotide sequence having at        least 80% sequence identity to a sequence as set forth in Table        1, in the section entitled “The predicted promoter sequence” or        fragment thereof; and    -   (3) a polynucleotide having a nucleotide sequence which        hybridizes to a sequence as set forth in Table 1, in the section        entitled “The predicted promoter sequence” under a condition        establishing a Tm−20° C.

Promoter or promoter control element sequences of the present inventionare capable of modulating preferential transcription.

In another embodiment, the present promoter control elements are capableof serving as or fulfilling the function, for example, as a corepromoter, a TATA box, a polymerase binding site, an initiator site, atranscription binding site, an enhancer, an inverted repeat, a locuscontrol region, or a scaffold/matrix attachment region.

It is yet another object of the present invention to provide apolynucleotide that includes at least a first and a second promotercontrol element. The first promoter control element is a promotercontrol element sequence as discussed above, and the second promotercontrol element is heterologous to the first control element. Moreover,the first and second control elements are operably linked. Suchpromoters may modulate transcript levels preferentially in a tissue orunder particular conditions.

In another embodiment, the present isolated polynucleotide comprises apromoter or a promoter control element as described above, wherein thepromoter or promoter control element is operably linked to apolynucleotide to be transcribed.

In another embodiment of the present vector, the promoter and promotercontrol elements of the instant invention are operably linked to aheterologous polynucleotide that is a regulatory sequence.

It is another object of the present invention to provide a host cellcomprising an isolated polynucleotide or vector as described above orfragment thereof. Host cells include, for instance, bacterial, yeast,insect, mammalian, and plant. The host cell can comprise a promoter orpromoter control element exogenous to the genome. Such a promoter canmodulate transcription in cis- and in trans-.

In yet another embodiment, the present host cell is a plant cell capableof regenerating into a plant.

It is yet another embodiment of the present invention to provide a plantcomprising an isolated polynucleotide or vector described above.

It is another object of the present invention to provide a method ofmodulating transcription in a sample that contains either a cell-freesystem of transcription or host cell. This method comprises providing apolynucleotide or vector according to the present invention as describedabove, and contacting the sample of the polynucleotide or vector withconditions that permit transcription.

In another embodiment of the present method, the polynucleotide orvector preferentially modulates

(a) constitutive transcription,

(b) stress induced transcription,

(c) light induced transcription,

(d) dark induced transcription,

(e) leaf transcription,

(f) root transcription,

(g) stem or shoot transcription,

(h) silique transcription,

(i) callus transcription,

(j) flower transcription,

(k) immature bud and inflorescence specific transcription, or

(l) senescing induced transcription

(m) germination transcription.

Other and further objects of the present invention will be made clear orbecome apparent from the following description.

BRIEF DESCRIPTION OF THE TABLES AND FIGURES Table 1

Table 1 consists of the Expression Reports for each promoter of theinvention providing the nucleotide sequence for each promoter anddetails for expression driven by each of the nucleic acid promotersequences as observed in transgenic plants. The results are presented assummaries of the spatial expression, which provides information as togross and/or specific expression in various plant organs and tissues.The observed expression pattern is also presented, which gives detailsof expression during different generations or different developmentalstages within a generation. Additional information is provided regardingthe associated gene, the GenBank reference, the source organism of thepromoter, and the vector and marker genes used for the construct. Thefollowing symbols are used consistently throughout the Table:

T1: First generation transformant

T2: Second generation transformant

T3: Third generation transformant

(L): low expression level

(M): medium expression level

(H): high expression level

Each row of the table begins with heading of the data to be found in thesection. The following provides a description of the data to be found ineach section:

Heading in Table 1 Description Promoter Identifies the particularpromoter by its construct ID. Modulates the gene: This row states thename of the gene modulated by the promoter The GenBank description ofthe gene: This field gives the Locus Number of the gene as well as theaccession number. The predicted promoter sequence: Identifies thenucleic acid promoter sequence in question. The promoter was cloned fromthe organism: Identifies the source of the DNA template used to clonethe promoter. The experimental promoter sequence: Identifies the nucleicacid sequence in planta driving expression of the reporter gene. Thepromoter was cloned in the vector: Identifies the vector used into whicha promoter was cloned. When cloned into the vector the promoter wasIdentifies the type of marker linked to the promoter. operably linked toa marker, which was the type: The marker is used to determine patternsof gene expression in plant tissue. Promoter-marker vector was testedin: Identifies the organism in which the promoter- marker vector wastested. Generation screened: T1 Mature T2 Identifies the plantgeneration(s) used in the Seedling T2 Mature T3 Seedling screeningprocess. T1 plants are those plants subjected to the transformationevent while the T2 generation plants are from the seeds collected fromthe T1 plants and T3 plants are from the seeds of T2 plants. The spatialexpression of the promoter-marker Identifies the specific parts of theplant where vector was found observed in and would be useful in variouslevels of GFP expression are observed. expression in any or all of thefollowing: Expression levels are noted as either low (L), medium (M), orhigh (H). Observed expression pattern of the promoter-marker Identifiesa general explanation of where GFP vector was in: expression indifferent generations of plants was T1 mature: observed. T2 seedling:The promoter can be of use in the following trait Identifies whichtraits and subtraits the promoter and sub-trait areas: (search for thetrait and sub-trait cDNA can modulate table) The promoter has utilityin: Identifies a specific function or functions that can be modulatedusing the promoter cDNA. Misc. promoter information: “Bidirectionality”is determined by the number of Bidirectionality: base pairs between thepromoter and the start codon Exons: of a neighboring gene. A promoter isconsidered Repeats: bidirectional if it is closer than 200 bp to a startcodon of a gene 5′ or 3′ to the promoter. “Exons” (or any codingsequence) identifies if the promoter has overlapped with either themodulating gene's or other neighboring gene's coding sequence. A “fail”for exons means that this overlap has occurred. “Repeats” identifies thepresence of normally occurring sequence repeats that randomly existthroughout the genome. A “pass” for repeats indicates a lack of repeatsin the promoter. An overlap in an exon with the endogenous codingIdentifies the specific nucleotides overlapping the sequence to thepromoter occurs at base pairs: UTR region or exon of a neighboring gene.The orientation relative to the promoter is designated with a 5′ or 3′.The Ceres cDNA ID of the endogenous coding Identifies the numberassociated with the Ceres sequence to the promoter: cDNA thatcorresponds to the endogenous cDNA sequence of the promoter. cDNAnucleotide sequence: The nucleic acid sequence of the Ceres cDNAmatching the endogenous cDNA region of the promoter. Coding sequence: Atranslated protein sequence of the gene modulated by a protein encodedby a cDNA Microarray Data shows that the coding sequence Microarray datais identified along with the was expressed in the following experiments,which corresponding experiments along with the shows that the promoterwould useful to modulate corresponding gene expression. Gene expressionis expression in situations similar to the following: identified by a“+” or a “−” in the “SIGN(LOG_RATIO)” column. A “+” notation indicatesthe cDNA is upregulated while a “−” indicates that the cDNA isdownregulated. The “SHORT_NAME” field describes the experimentalconditions. The parameters for the microarray experiments Parameters formicroarray experiments include age, listed above by EXPT_REP_ID andShort_Name organism, specific tissues, age, treatments and other are asfollow below: distinguishing characteristics or features.

Table 2

Table 1 provides the results of differential expression experimentsindicating if the expression levels were increased (“+”) or decreased(“−”). Such increase or decrease expression levels indicates the utilityof the corresponding promoter. The following Table 2 correlates thevarious differential expression experiments with the utility for thepromoter that would be understood from an increased or decreasedexpression. Table 2 includes three columns, the first column(“EXPT_REP_ID”) lists the microarray experiments by their experimentalprep ID number and correspond to the same number listings in Table 1 inthe “Microarray data” section. The second column lists the Short_Name ofthe experiment that corresponds to the EXPT_REP_if D. When a cDNA isdifferentially expressed in an experiment, identified by itsEXPT_REP_ID, the cDNA and its endogenous promoter can be used tomodulate the traits and subtraits listed in the third column.

FIG. 1

FIG. 1 is a schematic representation of the vector pNewBin4-HAP1-GFP.The definitions of the abbreviations used in the vector map are asfollows:

-   Ori—the origin of replication used by an E. coli host-   RB—sequence for the right border of the T-DNA from pMOG800-   BstXI—restriction enzyme cleavage site used for cloning-   HAP1VP16—coding sequence for a fusion protein of the HAP1 and VP16    activation domains-   NOS—terminator region from the nopaline synthase gene-   HAP1UAS—the upstream activating sequence for HAP1-   5ERGFP—the green fluorescent protein gene that has been optimized    for localization to the endoplasmic reticulum-   OCS2—the terminator sequence from the octopine synthase 2 gene-   OCS—the terminator sequence from the octopine synthase gene-   p28716 (a.k.a 28716 short)—promoter used to drive expression of the    PAT (BAR) gene-   PAT (BAR)—a marker gene conferring herbicide resistance-   LB—sequence for the left border of the T-DNA from pMOG800-   Spec—a marker gene conferring spectinomycin resistance-   TrfA—transcription repression factor gene-   RK2-OriV—origin of replication for Agrobacterium

DETAILED DESCRIPTION OF THE INVENTION 1. Definitions

Chimeric: The term “chimeric” is used to describe polynucleotides orgenes, as defined supra, or constructs wherein at least two of theelements of the polynucleotide or gene or construct, such as thepromoter and the polynucleotide to be transcribed and/or otherregulatory sequences and/or filler sequences and/or complements thereof,are heterologous to each other.

Constitutive Promoter: Promoters referred to herein as “constitutivepromoters” actively promote transcription under most, but notnecessarily all, environmental conditions and states of development orcell differentiation. Examples of constitutive promoters include thecauliflower mosaic virus (CaMV) 35S transcript initiation region and the1′ or 2′ promoter derived from T-DNA of Agrobacterium tumefaciens, andother transcription initiation regions from various plant genes, such asthe maize ubiquitin-1 promoter, known to those of skill.

Core Promoter: This is the minimal stretch of contiguous DNA sequencethat is sufficient to direct accurate initiation of transcription by theRNA polymerase II machinery (for review see: Struhl, 1987, Cell 49:295-297; Smale, 1994, In Transcription: Mechanisms and Regulation (edsR. C. Conaway and J. W. Conaway), pp 63-81/Raven Press, Ltd., New York;Smale, 1997, Biochim. Biophys. Acta 1351: 73-88; Smale et al., 1998,Cold Spring Harb. Symp. Quant. Biol. 58: 21-31; Smale, 2001, Genes &Dev. 15: 2503-2508; Weis and Reinberg, 1992, FASEB J. 6: 3300-3309;Burke et al., 1998, Cold Spring Harb. Symp. Quant. Biol 63: 75-82).There are several sequence motifs, including the TATA box, initiator(Inr), TFIIB recognition element (BRE) and downstream core promoterelement (DPE), that are commonly found in core promoters, however notall of these elements occur in all promoters and there are no universalcore promoter elements (Butler and Kadonaga, 2002, Genes & Dev. 16:2583-2592).

Domain: Domains are fingerprints or signatures that can be used tocharacterize protein families and/or parts of proteins. Suchfingerprints or signatures can comprise conserved (1) primary sequence,(2) secondary structure, and/or (3) three-dimensional conformation. Asimilar analysis can be applied to polynucleotides. Generally, eachdomain has been associated with either a conserved primary sequence or asequence motif. Generally these conserved primary sequence motifs havebeen correlated with specific in vitro and/or in vivo activities. Adomain can be any length, including the entirety of the polynucleotideto be transcribed. Examples of domains include, without limitation, AP2,helicase, homeobox, zinc finger, etc.

Endogenous: The term “endogenous,” within the context of the currentinvention refers to any polynucleotide, polypeptide or protein sequencewhich is a natural part of a cell or organisms regenerated from saidcell. In the context of promoter, the term “endogenous coding region” or“endogenous cDNA” refers to the coding region that is naturally operablylinked to the promoter.

Enhancer/Suppressor: An “enhancer” is a DNA regulatory element that canincrease the steady state level of a transcript, usually by increasingthe rate of transcription initiation. Enhancers usually exert theireffect regardless of the distance, upstream or downstream location, ororientation of the enhancer relative to the start site of transcription.In contrast, a “suppressor” is a corresponding DNA regulatory elementthat decreases the steady state level of a transcript, again usually byaffecting the rate of transcription initiation. The essential activityof enhancer and suppressor elements is to bind a protein factor(s). Suchbinding can be assayed, for example, by methods described below. Thebinding is typically in a manner that influences the steady state levelof a transcript in a cell or in an in vitro transcription extract.

Exogenous: As referred to within, “exogenous” is any polynucleotide,polypeptide or protein sequence, whether chimeric or not, that isintroduced into the genome of a host cell or organism regenerated fromsaid host cell by any means other than by a sexual cross. Examples ofmeans by which this can be accomplished are described below, and includeAgrobacterium-mediated transformation (of dicots—e.g. Salomon et al.EMBO J. 3:141 (1984); Herrera-Estrella et al. EMBO J. 2:987 (1983); ofmonocots, representative papers are those by Escudero et al., Plant J.10:355 (1996), Ishida et al., Nature Biotechnology 14:745 (1996), May etal., Bio/Technology 13:486 (1995)), biolistic methods (Armaleo et al.,Current Genetics 17:97 1990)), electroporation, in planta techniques,and the like. Such a plant containing the exogenous nucleic acid isreferred to here as a T₀ for the primary transgenic plant and T₁ for thefirst generation. The term “exogenous” as used herein is also intendedto encompass inserting a naturally found element into a non-naturallyfound location.

Gene: The term “gene,” as used in the context of the current invention,encompasses all regulatory and coding sequence contiguously associatedwith a single hereditary unit with a genetic function. Genes can includenon-coding sequences that modulate the genetic function that include,but are not limited to, those that specify polyadenylation,transcriptional regulation, DNA conformation, chromatin conformation,extent and position of base methylation and binding sites of proteinsthat control all of these. Genes encoding proteins are comprised of“exons” (coding sequences), which may be interrupted by “introns”(non-coding sequences). In some instances complexes of a plurality ofprotein or nucleic acids or other molecules, or of any two of the above,may be required for a gene's function. On the other hand a gene'sgenetic function may require only RNA expression or protein production,or may only require binding of proteins and/or nucleic acids withoutassociated expression. In certain cases, genes adjacent to one anothermay share sequence in such a way that one gene will overlap the other. Agene can be found within the genome of an organism, in an artificialchromosome, in a plasmid, in any other sort of vector, or as a separateisolated entity.

Heterologous sequences: “Heterologous sequences” are those that are notoperatively linked or are not contiguous to each other in nature. Forexample, a promoter from corn is considered heterologous to anArabidopsis coding region sequence. Also, a promoter from a geneencoding a growth factor from corn is considered heterologous to asequence encoding the corn receptor for the growth factor. Regulatoryelement sequences, such as UTRs or 3′ end termination sequences that donot originate in nature from the same gene as the coding sequenceoriginates from, are considered heterologous to said coding sequence.Elements operatively linked in nature and contiguous to each other arenot heterologous to each other.

Homologous: In the current invention, a “homologous” gene orpolynucleotide or polypeptide refers to a gene or polynucleotide orpolypeptide that shares sequence similarity with the gene orpolynucleotide or polypeptide of interest. This similarity may be inonly a fragment of the sequence and often represents a functional domainsuch as, examples including without limitation a DNA binding domain or adomain with tyrosine kinase activity. The functional activities ofhomologous polynucleotide are not necessarily the same.

Inducible Promoter: An “inducible promoter” in the context of thecurrent invention refers to a promoter, the activity of which isinfluenced by certain conditions, such as light, temperature, chemicalconcentration, protein concentration, conditions in an organism, cell,or organelle, etc. A typical example of an inducible promoter, which canbe utilized with the polynucleotides of the present invention, isPARSK1, the promoter from an Arabidopsis gene encoding aserine-threonine kinase enzyme, and which promoter is induced bydehydration, abscissic acid and sodium chloride (Wang and Goodman, PlantJ. 8:37 (1995)). Examples of environmental conditions that may affecttranscription by inducible promoters include anaerobic conditions,elevated temperature, the presence or absence of a nutrient or otherchemical compound or the presence of light.

Modulate Transcription Level: As used herein, the phrase “modulatetranscription” describes the biological activity of a promoter sequenceor promoter control element. Such modulation includes, withoutlimitation, includes up- and down-regulation of initiation oftranscription, rate of transcription, and/or transcription levels.

Mutant: In the current invention, “mutant” refers to a heritable changein nucleotide sequence at a specific location. Mutant genes of thecurrent invention may or may not have an associated identifiablephenotype.

Operable Linkage: An “operable linkage” is a linkage in which a promotersequence or promoter control element is connected to a polynucleotidesequence (or sequences) in such a way as to place transcription of thepolynucleotide sequence under the influence or control of the promoteror promoter control element. Two DNA sequences (such as a polynucleotideto be transcribed and a promoter sequence linked to the 5′ end of thepolynucleotide to be transcribed) are said to be operably linked ifinduction of promoter function results in the transcription of mRNAencoding the polynucleotide and if the nature of the linkage between thetwo DNA sequences does not (1) result in the introduction of aframe-shift mutation, (2) interfere with the ability of the promotersequence to direct the expression of the protein, antisense RNA orribozyme, or (3) interfere with the ability of the DNA template to betranscribed. Thus, a promoter sequence would be operably linked to apolynucleotide sequence if the promoter was capable of effectingtranscription of that polynucleotide sequence.

Optional Promoter Fragments: The phrase “optional promoter fragments” isused to refer to any sub-sequence of the promoter that is not requiredfor driving transcription of an operationally linked coding region.These fragments comprise the 5′ UTR and any exon(s) of the endogenouscoding region. The optional promoter fragments may also comprise anyexon(s) and the 3′ or 5′ UTR of the gene residing upstream of thepromoter (that is, 5′ to the promoter). Optional promoter fragments alsoinclude any intervening sequences that are introns or sequence thatoccurs between exons or an exon and the UTR.

Orthologous: “Orthologous” is a term used herein to describe arelationship between two or more polynucleotides or proteins. Twopolynucleotides or proteins are “orthologous” to one another if theyserve a similar function in different organisms. In general, orthologouspolynucleotides or proteins will have similar catalytic functions (whenthey encode enzymes) or will serve similar structural functions (whenthey encode proteins or RNA that form part of the ultrastructure of acell).

Percentage of sequence identity: “Percentage of sequence identity,” asused herein, is determined by comparing two optimally aligned sequencesover a comparison window, where the fragment of the polynucleotide oramino acid sequence in the comparison window may comprise additions ordeletions (e.g., gaps or overhangs) as compared to the referencesequence (which does not comprise additions or deletions) for optimalalignment of the two sequences. The percentage is calculated bydetermining the number of positions at which the identical nucleic acidbase or amino acid residue occurs in both sequences to yield the numberof matched positions, dividing the number of matched positions by thetotal number of positions in the window of comparison and multiplyingthe result by 100 to yield the percentage of sequence identity. Optimalalignment of sequences for comparison may be conducted by the localhomology algorithm of Smith and Waterman Add. APL. Math. 2:482 (1981),by the homology alignment algorithm of Needleman and Wunsch J. Mol.Biol. 48:443 (1970), by the search for similarity method of Pearson andLipman Proc. Natl. Acad. Sci. (USA) 85: 2444 (1988), by computerizedimplementations of these algorithms (GAP, BESTFIT, BLAST, PASTA, andTFASTA in the Wisconsin Genetics Software Package, Genetics ComputerGroup (GCG), 575 Science Dr., Madison, Wis.), or by inspection. Giventhat two sequences have been identified for comparison, GAP and BESTFITare preferably employed to determine their optimal alignment. Typically,the default values of 5.00 for gap weight and 0.30 for gap weight lengthare used.

Plant Promoter: A “plant promoter” is a promoter capable of initiatingtranscription in plant cells and can modulate transcription of apolynucleotide. Such promoters need not be of plant origin. For example,promoters derived from plant viruses, such as the CaMV35S promoter orfrom Agrobacterium tumefaciens such as the T-DNA promoters, can be plantpromoters. A typical example of a plant promoter of plant origin is themaize ubiquitin-1 (ubi-1) promoter known to those of skill.

Plant Tissue: The term “plant tissue” includes differentiated andundifferentiated tissues or plants, including but not limited to roots,stems, shoots, cotyledons, epicotyl, hypocotyl, leaves, pollen, seeds,tumor tissue and various forms of cells in culture such as single cells,protoplast, embryos, and callus tissue. The plant tissue may be inplants or in organ, tissue or cell culture.

Preferential Transcription: “Preferential transcription” is defined astranscription that occurs in a particular pattern of cell types ordevelopmental times or in response to specific stimuli or combinationthereof. Non-limitive examples of preferential transcription include:high transcript levels of a desired sequence in root tissues; detectabletranscript levels of a desired sequence in certain cell types duringembryogenesis; and low transcript levels of a desired sequence underdrought conditions. Such preferential transcription can be determined bymeasuring initiation, rate, and/or levels of transcription.

Promoter: A “promoter” is a DNA sequence that directs the transcriptionof a polynucleotide. Typically a promoter is located in the 5′ region ofa polynucleotide to be transcribed, proximal to the transcriptionalstart site of such polynucleotide. More typically, promoters are definedas the region upstream of the first exon; more typically, as a regionupstream of the first of multiple transcription start sites; moretypically, as the region downstream of the preceding gene and upstreamof the first of multiple transcription start sites; more typically, theregion downstream of the polyA signal and upstream of the first ofmultiple transcription start sites; even more typically, about 3,000nucleotides upstream of the ATG of the first exon; even more typically,2,000 nucleotides upstream of the first of multiple transcription startsites. The promoters of the invention comprise at least a core promoteras defined above. Frequently promoters are capable of directingtranscription of genes located on each of the complementary DNA strandsthat are 3′ to the promoter. Stated differently, many promoters exhibitbidirectionality and can direct transcription of a downstream gene whenpresent in either orientation (i.e. 5′ to 3′ or 3′ to 5′ relative to thecoding region of the gene). Additionally, the promoter may also includeat least one control element such as an upstream element. Such elementsinclude UARs and optionally, other DNA sequences that affecttranscription of a polynucleotide such as a synthetic upstream element.

Promoter Control Element: The term “promoter control element” as usedherein describes elements that influence the activity of the promoter.Promoter control elements include transcriptional regulatory sequencedeterminants such as, but not limited to, enhancers, scaffold/matrixattachment regions, TATA boxes, transcription start locus controlregions, UARs, URRs, other transcription factor binding sites andinverted repeats.

Public sequence: The term “public sequence,” as used in the context ofthe instant application, refers to any sequence that has been depositedin a publicly accessible database prior to the filing date of thepresent application. This term encompasses both amino acid andnucleotide sequences. Such sequences are publicly accessible, forexample, on the BLAST databases on the NCBI FTP web site (accessible atncbi.nlm.nih.gov/ftp). The database at the NCBI FTP site utilizes “gi”numbers assigned by NCBI as a unique identifier for each sequence in thedatabases, thereby providing a non-redundant database for sequence fromvarious databases, including GenBank, EMBL, DBBJ, (DNA Database ofJapan) and PDB (Brookhaven Protein Data Bank).

Regulatory Sequence The term “regulatory sequence,” as used in thecurrent invention, refers to any nucleotide sequence that influencestranscription or translation initiation and rate, or stability and/ormobility of a transcript or polypeptide product. Regulatory sequencesinclude, but are not limited to, promoters, promoter control elements,protein binding sequences, 5′ and 3′ UTRs, transcriptional start sites,termination sequences, polyadenylation sequences, introns, certainsequences within amino acid coding sequences such as secretory signals,protease cleavage sites, etc.

Related Sequences: “Related sequences” refer to either a polypeptide ora nucleotide sequence that exhibits some degree of sequence similaritywith a reference sequence.

Specific Promoters: In the context of the current invention, “specificpromoters” refers to a subset of promoters that have a high preferencefor modulating transcript levels in a specific tissue or organ or celland/or at a specific time during development of an organism. By “highpreference” is meant at least 3-fold, preferably 5-fold, more preferablyat least 10-fold still more preferably at least 20-fold, 50-fold or100-fold increase in transcript levels under the specific condition overthe transcription under any other reference condition considered.Typical examples of temporal and/or tissue or organ specific promotersof plant origin that can be used with the polynucleotides of the presentinvention, are: PTA29, a promoter which is capable of driving genetranscription specifically in tapetum and only during anotherdevelopment (Koltonow et al., Plant Cell 2:1201 (1990); RCc2 and RCc3,promoters that direct root-specific gene transcription in rice (Xu etal., Plant Mol. Biol. 27:237 (1995); TobRB27, a root-specific promoterfrom tobacco (Yamamoto et al., Plant Cell 3:371 (1991)). Examples oftissue-specific promoters under developmental control include promotersthat initiate transcription only in certain tissues or organs, such asroot, ovule, fruit, seeds, or flowers. Other specific promoters includethose from genes encoding seed storage proteins or the lipid bodymembrane protein, oleosin. A few root-specific promoters are notedabove. See also “Preferential transcription”.

Stringency: “Stringency” as used herein is a function of probe length,probe composition (G+C content), and salt concentration, organic solventconcentration, and temperature of hybridization or wash conditions.Stringency is typically compared by the parameter T_(m), which is thetemperature at which 50% of the complementary molecules in thehybridization are hybridized, in terms of a temperature differentialfrom T_(m). High stringency conditions are those providing a conditionof T_(m)−5° C. to T_(m)−10° C. Medium or moderate stringency conditionsare those providing T_(m)−20° C. to T_(m)−29° C. Low stringencyconditions are those providing a condition of T_(m)−40° C. to T_(m)−48°C. The relationship of hybridization conditions to T_(m) (in ° C.) isexpressed in the mathematical equationT _(m)=81.5−16.6(log₁₀[Na⁺])+0.41(% G+C)−(600/N)  (1)where N is the length of the probe. This equation works well for probes14 to 70 nucleotides in length that are identical to the targetsequence. The equation below for T_(m) of DNA-DNA hybrids is useful forprobes in the range of 50 to greater than 500 nucleotides, and forconditions that include an organic solvent (formamide).T _(m)=81.5+16.6 log {[Na⁺]/(1+0.7[Na⁺])}+0.41(% G+C)−500/L 0.63(%formamide)  (2)where L is the length of the probe in the hybrid. (P. Tijessen,“Hybridization with Nucleic Acid Probes” in Laboratory Techniques inBiochemistry and Molecular Biology, P. C. vand der Vliet, ed., c. 1993by Elsevier, Amsterdam.) The T_(m) of equation (2) is affected by thenature of the hybrid; for DNA-RNA hybrids T_(m) is 10-15° C. higher thancalculated, for RNA-RNA hybrids T_(m) is 20-25° C. higher. Because theT_(m) decreases about 1° C. for each 1% decrease in homology when a longprobe is used (Bonner et al., J. Mol. Biol. 81:123 (1973)), stringencyconditions can be adjusted to favor detection of identical genes orrelated family members.

Equation (2) is derived assuming equilibrium and therefore,hybridizations according to the present invention are most preferablyperformed under conditions of probe excess and for sufficient time toachieve equilibrium. The time required to reach equilibrium can beshortened by inclusion of a hybridization accelerator such as dextransulfate or another high volume polymer in the hybridization buffer.

Stringency can be controlled during the hybridization reaction or afterhybridization has occurred by altering the salt and temperatureconditions of the wash solutions used. The formulas shown above areequally valid when used to compute the stringency of a wash solution.Preferred wash solution stringencies lie within the ranges stated above;high stringency is 5-8° C. below T_(m), medium or moderate stringency is26-29° C. below T_(m) and low stringency is 45-48° C. below T_(m).

Substantially free of: A composition containing A is “substantially freeof” B when at least 85% by weight of the total A+B in the composition isA. Preferably, A comprises at least about 90% by weight of the total ofA+B in the composition, more preferably at least about 95% or even 99%by weight. For example, a plant gene can be substantially free of otherplant genes. Other examples include, but are not limited to, ligandssubstantially free of receptors (and vice versa), a growth factorsubstantially free of other growth factors and a transcription bindingfactor substantially free of nucleic acids.

Suppressor: See “Enhancer/Suppressor”

TATA to start: “TATA to start” shall mean the distance, in number ofnucleotides, between the primary TATA motif and the start oftranscription.

Transgenic plant: A “transgenic plant” is a plant having one or moreplant cells that contain at least one exogenous polynucleotideintroduced by recombinant nucleic acid methods.

Translational start site: In the context of the present invention, a“translational start site” is usually an ATG or AUG in a transcript,often the first ATG or AUG. A single protein encoding transcript,however, may have multiple translational start sites.

Transcription start site: “Transcription start site” is used in thecurrent invention to describe the point at which transcription isinitiated. This point is typically located about 25 nucleotidesdownstream from a TFIID binding site, such as a TATA box. Transcriptioncan initiate at one or more sites within the gene, and a singlepolynucleotide to be transcribed may have multiple transcriptional startsites, some of which may be specific for transcription in a particularcell-type or tissue or organ. “+1” is stated relative to thetranscription start site and indicates the first nucleotide in atranscript.

Upstream Activating Region (UAR): An “Upstream Activating Region” or“UAR” is a position or orientation dependent nucleic acid element thatprimarily directs tissue, organ, cell type, or environmental regulationof transcript level, usually by affecting the rate of transcriptioninitiation. Corresponding DNA elements that have a transcriptioninhibitory effect are called herein “Upstream Repressor Regions” or“URR”s. The essential activity of these elements is to bind a proteinfactor. Such binding can be assayed by methods described below. Thebinding is typically in a manner that influences the steady state levelof a transcript in a cell or in vitro transcription extract.

Untranslated region (UTR): A “UTR” is any contiguous series ofnucleotide bases that is transcribed, but is not translated. A 5′ UTRlies between the start site of the transcript and the translationinitiation codon and includes the +1 nucleotide. A 3′ UTR lies betweenthe translation termination codon and the end of the transcript. UTRscan have particular functions such as increasing mRNA message stabilityor translation attenuation. Examples of 3′ UTRs include, but are notlimited to polyadenylation signals and transcription terminationsequences.

Variant: The term “variant” is used herein to denote a polypeptide orprotein or polynucleotide molecule that differs from others of its kindin some way. For example, polypeptide and protein variants can consistof changes in amino acid sequence and/or charge and/orpost-translational modifications (such as glycosylation, etc). Likewise,polynucleotide variants can consist of changes that add or delete aspecific UTR or exon sequence. It will be understood that there may besequence variations within sequence or fragments used or disclosed inthis application. Preferably, variants will be such that the sequenceshave at least 80%, preferably at least 90%, 95, 97, 98, or 99% sequenceidentity. Variants preferably measure the primary biological function ofthe native polypeptide or protein or polynucleotide.

2. Introduction

The polynucleotides of the invention comprise promoters and promotercontrol elements that are capable of modulating transcription.

Such promoters and promoter control elements can be used in combinationwith native or heterologous promoter fragments, control elements orother regulatory sequences to modulate transcription and/or translation.

Specifically, promoters and control elements of the invention can beused to modulate transcription of a desired polynucleotide, whichincludes without limitation:

-   -   (a) antisense;    -   (b) ribozymes;    -   (c) coding sequences; or    -   (d) fragments thereof.        The promoter also can modulate transcription in a host genome in        cis- or in trans-.

In an organism, such as a plant, the promoters and promoter controlelements of the instant invention are useful to produce preferentialtranscription which results in a desired pattern of transcript levels ina particular cells, tissues, or organs, or under particular conditions.

3. Table of Contents

The following description of the present invention is outlined in thefollowing table of contents.

A. Identifying and Isolating Promoter Sequences of the Invention

-   -   (1) Cloning Methods    -   (2) Chemical Synthesis

B. Generating a “core” promoter sequence

C. Isolating Related Promoter Sequences

-   -   (1) Relatives Based on Nucleotide Sequence Identity    -   (2) Relatives Based on Coding Sequence Identity    -   (3) Relatives based on Common Function

D. Identifying Control Elements

-   -   (1) Types of Transcription Control Elements    -   (2) Those Described by the Examples    -   (3) Those Identifiable by Bioinformatics    -   (4) Those Identifiable by In Vitro and In Vivo Assays    -   (5) Non-Natural Control Elements

E. Constructing Promoters and Control Elements

-   -   (1) Combining Promoters and Promoter Control Elements    -   (2) Number of Promoter Control Elements    -   (3) Spacing Between Control Elements

F. Vectors

-   -   (1) Modification of Transcription by Promoters and Promoter        Control Elements    -   (2) Polynucleotide to be Transcribed    -   (3) Other Regulatory Elements    -   (4) Other Components of Vectors

G. Insertion of Polynucleotides and Vectors into a Host Cell

-   -   (1) Autonomous of the Host Genome    -   (2) Integrated into the Host Genome

H. Utility

A. Identifying and Isolating Promoter Sequences of the Invention

The promoters and promoter control elements of the present invention arepresented in Table 1 in the section entitled “The predicted promoter”sequence and were identified from Arabidopsis thaliana or Oryza sativa.Additional promoter sequences encompassed by the invention can beidentified as described below.

(1) Cloning Methods

Isolation from genomic libraries of polynucleotides comprising thesequences of the promoters and promoter control elements of the presentinvention is possible using known techniques.

For example, polymerase chain reaction (PCR) can amplify the desiredpolynucleotides utilizing primers designed from sequences in the rowtitled “The spatial expression of the promoter-marker-vector”.Polynucleotide libraries comprising genomic sequences can be constructedaccording to Sambrook et al., Molecular Cloning: A Laboratory Manual,2^(nd) Ed. (1989) Cold Spring Harbor Press, Cold Spring Harbor, N.Y.),for example.

Other procedures for isolating polynucleotides comprising the promotersequences of the invention include, without limitation, tail-PCR, and 5′rapid amplification of cDNA ends (RACE). See, for tail-PCR, for example,Liu et al., Plant J 8(3): 457-463 (September, 1995); Liu et al.,Genomics 25: 674-681 (1995); Liu et al., Nucl. Acids Res. 21(14):3333-3334 (1993); and Zoe et al., BioTechniques 27(2): 240-248 (1999);for RACE, see, for example, PCR Protocols: A Guide to Methods andApplications, (1990) Academic Press, Inc.

(2) Chemical Synthesis

In addition, the promoters and promoter control elements described inTable 1 in the section entitled “The predicted promoter” sequence can bechemically synthesized according to techniques in common use. See, forexample, Beaucage et al., Tet. Lett. (1981) 22: 1859 and U.S. Pat. No.4,668,777.

Such chemical oligonucleotide synthesis can be carried out usingcommercially available devices, such as, Biosearch 4600 or 8600 DNAsynthesizer, by Applied Biosystems, a division of Perkin-Elmer Corp.,Foster City, Calif., USA; and Expedite by Perceptive Biosystems,Framingham, Mass., USA.

Synthetic RNA, including natural and/or analog building blocks, can besynthesized on the Biosearch 8600 machines, see above.

Oligonucleotides can be synthesized and then ligated together toconstruct the desired polynucleotide.

B. Generating Reduced and “Core” Promoter Sequences

Included in the present invention are reduced and “core” promotersequences. The reduced promoters can be isolated from the promoters ofthe invention by deleting at least one 5′ UTR, exon or 3′ UTR sequencepresent in the promoter sequence that is associated with a gene orcoding region located 5′ to the promoter sequence or in the promoter'sendogenous coding region.

Similarly, the “core” promoter sequences can be generated by deletingall 5′ UTRs, exons and 3′ UTRs present in the promoter sequence and theassociated intervening sequences that are related to the gene or codingregion 5′ to the promoter region and the promoter's endogenous codingregion.

This data is presented in the row titled “Optional Promoter Fragments”.

C. Isolating Related Promoter Sequences

Included in the present invention are promoter and promoter controlelements that are related to those described in Table 1 in the sectionentitled “The predicted promoter sequence”. Such related sequence can beisolated utilizing

(a) nucleotide sequence identity;

(b) coding sequence identity; or

(c) common function or gene products.

Relatives can include both naturally occurring promoters and non-naturalpromoter sequences. Non-natural related promoters include nucleotidesubstitutions, insertions or deletions of naturally-occurring promotersequences that do not substantially affect transcription modulationactivity. For example, the binding of relevant DNA binding proteins canstill occur with the non-natural promoter sequences and promoter controlelements of the present invention.

According to current knowledge, promoter sequences and promoter controlelements exist as functionally important regions, such as proteinbinding sites, and spacer regions. These spacer regions are apparentlyrequired for proper positioning of the protein binding sites. Thus,nucleotide substitutions, insertions and deletions can be tolerated inthese spacer regions to a certain degree without loss of function.

In contrast, less variation is permissible in the functionally importantregions, since changes in the sequence can interfere with proteinbinding. Nonetheless, some variation in the functionally importantregions is permissible so long as function is conserved.

The effects of substitutions, insertions and deletions to the promotersequences or promoter control elements may be to increase or decreasethe binding of relevant DNA binding proteins to modulate transcriptlevels of a polynucleotide to be transcribed. Effects may includetissue-specific or condition-specific modulation of transcript levels ofthe polypeptide to be transcribed. Polynucleotides representing changesto the nucleotide sequence of the DNA-protein contact region byinsertion of additional nucleotides, changes to identity of relevantnucleotides, including use of chemically-modified bases, or deletion ofone or more nucleotides are considered encompassed by the presentinvention.

(1) Relatives Based on Nucleotide Sequence Identity

Included in the present invention are promoters exhibiting nucleotidesequence identity to those described in Table 1 in the section entitled“The predicted promoter sequence”.

Definition

Typically, such related promoters exhibit at least 80% sequenceidentity, preferably at least 85%, more preferably at least 90%, andmost preferably at least 95%, even more preferably, at least 96%, 97%,98% or 99% sequence identity compared to those shown in Table 1 in thesection entitled “The predicted promoter” sequence. Such sequenceidentity can be calculated by the algorithms and computers programsdescribed above.

Usually, such sequence identity is exhibited in an alignment region thatis at least 75% of the length of a sequence shown in Table 1 in thesection entitled “The predicted promoter” sequence or correspondingfull-length sequence; more usually at least 80%; more usually, at least85%, more usually at least 90%, and most usually at least 95%, even moreusually, at least 96%, 97%, 98% or 99% of the length of a sequence shownin Table 1 in the section entitled “The predicted promoter sequence”.

The percentage of the alignment length is calculated by counting thenumber of residues of the sequence in region of strongest alignment,e.g., a continuous region of the sequence that contains the greatestnumber of residues that are identical to the residues between twosequences that are being aligned. The number of residues in the regionof strongest alignment is divided by the total residue length of asequence in Table 1 in the section entitled “The predicted promotersequence”.

These related promoters may exhibit similar preferential transcriptionas those promoters described in Table 1 in the section entitled “Thepredicted promoter sequence”.

Construction of Polynucleotides

Naturally occurring promoters that exhibit nucleotide sequence identityto those shown in Table 1 in the section entitled “The predictedpromoter sequence” can be isolated using the techniques as describedabove. More specifically, such related promoters can be identified byvarying stringencies, as defined above, in typical hybridizationprocedures such as Southern blots or probing of polynucleotidelibraries, for example.

Non-natural promoter variants of those shown in Table 1 can beconstructed using cloning methods that incorporate the desirednucleotide variation. See, for example, Ho, S. N., et al. Gene 77:51-591989, describing a procedure site directed mutagenesis using PCR.

Any related promoter showing sequence identity to those shown in Tablecan be chemically synthesized as described above.

Also, the present invention includes non-natural promoters that exhibitthe above-sequence identity to those in Table 1.

The promoters and promoter control elements of the present invention mayalso be synthesized with 5′ or 3′ extensions, to facilitate additionalmanipulation, for instance.

The present invention also includes reduced promoter sequences. Thesesequences have at least one of the optional promoter fragments deleted.

Core promoter sequences are another embodiment of the present invention.The core promoter sequences have all of the optional promoter fragmentsdeleted.

Testing of Polynucleotides

Polynucleotides of the invention were tested for activity by cloning thesequence into an appropriate vector, transforming plants with theconstruct and assaying for marker gene expression. Recombinant DNAconstructs were prepared which comprise the polynucleotide sequences ofthe invention inserted into a vector suitable for transformation ofplant cells. The construct can be made using standard recombinant DNAtechniques (Sambrook et al. 1989) and can be introduced to the speciesof interest by Agrobacterium-mediated transformation or by other meansof transformation as referenced below.

The vector backbone can be any of those typical in the art such asplasmids, viruses, artificial chromosomes, BACs, YACs and PACs andvectors of the sort described by

-   (a) BAC: Shizuya et al., Proc. Natl. Acad. Sci. USA 89: 8794-8797    (1992); Hamilton et al., Proc. Natl. Acad. Sci. USA 93: 9975-9979    (1996);-   (b) YAC: Burke et al., Science 236:806-812 (1987);-   (c) PAC: Sternberg N. et al., Proc Natl Acad Sci USA. January;    87(1):103-7 (1990);-   (d) Bacteria-Yeast Shuttle Vectors: Bradshaw et al., Nucl Acids Res    23: 4850-4856 (1995);-   (e) Lambda Phage Vectors: Replacement Vector, e.g., Frischauf et    al., J. Mol Biol 170: 827-842 (1983); or Insertion vector, e.g.,    Huynh et al., In: Glover N M (ed) DNA Cloning: A practical Approach,    Vol. 1 Oxford: IRL Press (1985); T-DNA gene fusion vectors: Walden    et al., Mol Cell Biol 1: 175-194 (1990); and-   (g) Plasmid vectors: Sambrook et al., infra.

Typically, the construct comprises a vector containing a sequence of thepresent invention operationally linked to any marker gene. Thepolynucleotide was identified as a promoter by the expression of themarker gene. Although many marker genes can be used, Green FluorescentProtein (GFP) is preferred. The vector may also comprise a marker genethat confers a selectable phenotype on plant cells. The marker mayencode biocide resistance, particularly antibiotic resistance, such asresistance to kanamycin, G418, bleomycin, hygromycin, or herbicideresistance, such as resistance to chlorosulfuron or phosphinotricin.Vectors can also include origins of replication, scaffold attachmentregions (SARs), markers, homologous sequences, introns, etc.

Promoter Control Elements of the Invention

The promoter control elements of the present invention include thosethat comprise a sequence shown in Table 1 in the section entitled “Thepredicted promoter sequence” and fragments thereof. The size of thefragments of the row titled “The predicted promoter sequence” can rangefrom 5 bases to 10 kilobases (kb). Typically, the fragment size is nosmaller than 8 bases; more typically, no smaller than 12; moretypically, no smaller than 15 bases; more typically, no smaller than 20bases; more typically, no smaller than 25 bases; even more typically, nomore than 30, 35, 40 or 50 bases.

Usually, the fragment size in no larger than 5 kb bases; more usually,no larger than 2 kb; more usually, no larger than 1 kb; more usually, nolarger than 800 bases; more usually, no larger than 500 bases; even moreusually, no more than 250, 200, 150 or 100 bases.

Relatives Based on Nucleotide Sequence Identity

Included in the present invention are promoter control elementsexhibiting nucleotide sequence identity to those described in Table 1 inthe section entitled “The predicted promoter sequence” of fragmentsthereof.

Typically, such related promoters exhibit at least 80% sequenceidentity, preferably at least 85%, more preferably at least 90%, andmost preferably at least 95%, even more preferably, at least 96%, 97%,98% or 99% sequence identity compared to those shown in Table 1 in thesection entitled “The predicted promoter sequence”. Such sequenceidentity can be calculated by the algorithms and computers programsdescribed above.

Promoter Control Element Configuration

A common configuration of the promoter control elements in RNApolymerase II promoters is shown below:

For more description, see, for example, “Models for prediction andrecognition of eukaryotic promoters”, T. Werner, Mammalian Genome, 10,168-175 (1999).

Promoters are generally modular in nature. Promoters can consist of abasal promoter which functions as a site for assembly of a transcriptioncomplex comprising an RNA polymerase, for example RNA polymerase II. Atypical transcription complex will include additional factors such asTF_(II)B, TF_(II)D, and TF_(II)E. Of these, TF_(II)D appears to be theonly one to bind DNA directly. The promoter might also contain one ormore promoter control elements such as the elements discussed above.These additional control elements may function as binding sites foradditional transcription factors that have the function of modulatingthe level of transcription with respect to tissue specificity and oftranscriptional responses to particular environmental or nutritionalfactors, and the like.

One type of promoter control element is a polynucleotide sequencerepresenting a binding site for proteins. Typically, within a particularfunctional module, protein binding sites constitute regions of 5 to 60,preferably 10 to 30, more preferably 10 to 20 nucleotides. Within suchbinding sites, there are typically 2 to 6 nucleotides which specificallycontact amino acids of the nucleic acid binding protein.

The protein binding sites are usually separated from each other by 10 toseveral hundred nucleotides, typically by 15 to 150 nucleotides, oftenby 20 to 50 nucleotides.

Further, protein binding sites in promoter control elements oftendisplay dyad symmetry in their sequence. Such elements can bind severaldifferent proteins, and/or a plurality of sites can bind the sameprotein. Both types of elements may be combined in a region of 50 to1,000 base pairs.

Binding sites for any specific factor have been known to occur almostanywhere in a promoter. For example, functional AP-1 binding sites canbe located far upstream, as in the rat bone sialoprotein gene, where anAP-1 site located about 900 nucleotides upstream of the transcriptionstart site suppresses expression. Yamauchi et al., Matrix Biol., 15,119-130 (1996). Alternatively, an AP-1 site located close to thetranscription start site plays an important role in the expression ofMoloney murine leukemia virus. Sap et al., Nature, 340, 242-244, (1989).

(2) Those Identifiable by Bioinformatics

Promoter control elements from the promoters of the instant inventioncan be identified utilizing bioinformatic or computer driven techniques.

One method uses a computer program AlignACE to identify regulatorymotifs in genes that exhibit common preferential transcription across anumber of time points. The program identifies common sequence motifs insuch genes. See, Roth et al., Nature Biotechnol. 16: 949-945 (1998);Tavazoie et al., Nat Genet. 1999 July; 22(3):281-5;

Genomatix, also makes available a GEMS Launcher program and otherprograms to identify promoter control elements and configuration of suchelements. Genomatix is located in Munich, Germany.

Other references also describe detection of promoter modules by modelsindependent of overall nucleotide sequence similarity. See, forinstance, Klingenhoff et al., Bioinformatics 15, 180-186 (1999).

Protein binding sites of promoters can be identified as reported in“Computer-assisted prediction, classification, and delimination ofprotein binding sites in nucleic acids”, Frech, et al., Nucleic AcidsResearch, Vol. 21, No. 7, 1655-1664, 1993.

Other programs used to identify protein binding sites include, forexample, Signal Scan, Prestridge et al., Comput. Appl, Biosci. 12:157-160 (1996); Matrix Search, Chen et al., Comput. Appl. Biosci. 11:563-566 (1995), available as part of Signal Scan 4.0; MatInspector,Ghosh et al., Nucl, Acid Res, 21: 3117-3118 (1993) available on theinternet; ConsInspector, Frech et al., Nucl, Acids Res, 21: 1655-1664(1993), available at ftp://ariane.gsf.de/pub/dos; TFSearch; and TESS.

Frech et al., “Software for the analysis of DNA sequence elements oftranscription”, Bioinformatics & Sequence Analysis, Vol. 13, no. 1,89-97 (1997) is a review of different software for analysis of promotercontrol elements. This paper also reports the usefulness of matrix-basedapproaches to yield more specific results.

For other procedures, see, Fickett et al., Curr. Op. Biotechnol. 11:19-24 (2000); and Quandt et al., Nucleic Acids Res., 23, 4878-4884(1995).

(3) Those Identifiable by In-Vitro and In-Vivo Assays

Promoter control elements also can be identified with in-vitro assays,such as transcription detection methods; and with in-vivo assays, suchas enhancer trapping protocols.

In-Vitro Assays

Examples of in-vitro assays include detection of binding of proteinfactors that bind promoter control elements. Fragments of the instantpromoters can be used to identify the location of promoter controlelements. Another option for obtaining a promoter control element withdesired properties is to modify known promoter sequences. This is basedon the fact that the function of a promoter is dependent on theinterplay of regulatory proteins that bind to specific, discretenucleotide sequences in the promoter, termed motifs. Such interplaysubsequently affects the general transcription machinery and regulatestranscription efficiency. These proteins are positive regulators ornegative regulators (repressors), and one protein can have a dual roledepending on the context (Johnson, P. F. and McKnight, S. L. Annu. Rev.Biochem. 58:799-839 (1989)).

One type of in-vitro assay utilizes a known DNA binding factor toisolate DNA fragments that bind. If a fragment or promoter variant doesnot bind, then a promoter control element has been removed or disrupted.For specific assays, see, for instance, B. Luo et al., J. Mol. Biol.266:470 (1997), S. Chusacultanachai et al., J. Biol. Chem. 274:23591(1999), D. Fabbro et al., Biochem. Biophys. Res. Comm. 213:781 (1995)).

Alternatively, a fragment of DNA suspected of conferring a particularpattern of specificity can be examined for activity in bindingtranscription factors involved in that specificity by methods such asDNA footprinting (e.g. D. J. Cousins et al., Immunology 99:101 (2000);V. Kolla et al., Biochem. Biophys. Res. Comm. 266:5 (1999)) or“mobility-shift” assays (E. D. Fabiani et al., J. Biochem. 347:147(2000); N. Sugiura et al., J. Biochem 347:155 (2000)) or fluorescencepolarization (e.g. Royer et al., U.S. Pat. No. 5,445,935). Both mobilityshift and DNA footprinting assays can also be used to identify portionsof large DNA fragments that are bound by proteins in unpurifiedtranscription extracts prepared from tissues or organs of interest.

Cell-free transcription extracts can be prepared and used to directlyassay in a reconstitutable system (Narayan et al., Biochemistry 39:818(2000)).

In-Vivo Assays

Promoter control elements can be identified with reporter genes inin-vivo assays with the use of fragments of the instant promoters orvariants of the instant promoter polynucleotides.

For example, various fragments can be inserted into a vector, comprisinga basal or “core” promoter, for example, operably linked to a reportersequence, which, when transcribed, can produce a detectable label.Examples of reporter genes include those encoding luciferase, greenfluorescent protein, GUS, neo, cat and bar. Alternatively, reportersequence can be detected utilizing AFLP and microarray techniques.

In promoter probe vector systems, genomic DNA fragments are insertedupstream of the coding sequence of a reporter gene that is expressedonly when the cloned fragment contains DNA having transcriptionmodulation activity (Neve, R. L. et al., Nature 277:324-325 (1979)).Control elements are disrupted when fragments or variants lacking anytranscription modulation activity. Probe vectors have been designed forassaying transcription modulation in E. coli (An, G. et al., J. Bact.140:400-407 (1979)) and other bacterial hosts (Band, L. et al., Gene26:313-315 (1983); Achen, M. G., Gene 45:45-49 (1986)), yeast (Goodey,A. R. et al., Mol. Gen. Genet. 204:505-511 (1986)) and mammalian cells(Pater, M. M. et al., J. Mol. App. Gen. 2:363-371 (1984)).

A different design of a promoter/control element trap includes packaginginto retroviruses for more efficient delivery into cells. One type ofretroviral enhancer trap was described by von Melchner et al. (GenesDev. 1992; U.S. Pat. No. 5,364,783). The basic design of this vectorincludes a reporter protein coding sequence engineered into the U3portion of the 3′ LTR. No splice acceptor consensus sequences areincluded, limiting its utility to work as an enhancer trap only. Adifferent approach to a gene trap using retroviral vectors was pursuedby Friedrich and Soriano (Genes Dev. 1991), who engineered a lacZ-neofusion protein linked to a splicing acceptor. LacZ-neo fusion proteinexpression from trapped loci allows not only for drug selection, butalso for visualization of β-galatactosidase expression using thechromogenic substrate, X-gal.

A general review of tools for identifying transcriptional regulatoryregions of genomic DNA is provided by J. W. Fickett et al. (Curr. Opn.Biotechnol. 11:19 (2000).

(4) Non-Natural Control Elements

Non-natural control elements can be constructed by inserting, deletingor substituting nucleotides into the promoter control elements describedabove. Such control elements are capable of transcription modulationthat can be determined using any of the assays described above.

D. Constructing Promoters with Control Elements

(1) Combining Promoters and Promoter Control Elements

The promoter polynucleotides and promoter control elements of thepresent invention, both naturally occurring and synthetic, can becombined with each other to produce the desired preferentialtranscription. Also, the polynucleotides of the invention can becombined with other known sequences to obtain other useful promoters tomodulate, for example, tissue transcription specific or transcriptionspecific to certain conditions. Such preferential transcription can bedetermined using the techniques or assays described above.

Fragments, variants, as well as full-length sequences those shown inTable 1 in the section entitled “The predicted promoter sequence” andrelatives are useful alone or in combination.

The location and relation of promoter control elements within a promotercan affect the ability of the promoter to modulate transcription. Theorder and spacing of control elements is a factor when constructingpromoters.

(2) Number of Promoter Control Elements

Promoters can contain any number of control elements. For example, apromoter can contain multiple transcription binding sites or othercontrol elements. One element may confer tissue or organ specificity;another element may limit transcription to specific time periods, etc.Typically, promoters will contain at least a basal or core promoter asdescribed above. Any additional element can be included as desired. Forexample, a fragment comprising a basal or “core” promoter can be fusedwith another fragment with any number of additional control elements.

(3) Spacing Between Control Elements

Spacing between control elements or the configuration or controlelements can be determined or optimized to permit the desiredprotein-polynucleotide or polynucleotide interactions to occur.

For example, if two transcription factors bind to a promotersimultaneously or relatively close in time, the binding sites are spacedto allow each factor to bind without steric hinderance. The spacingbetween two such hybridizing control elements can be as small as aprofile of a protein bound to a control element. In some cases, twoprotein binding sites can be adjacent to each other when the proteinsbind at different times during the transcription process.

Further, when two control elements hybridize the spacing between suchelements will be sufficient to allow the promoter polynucleotide tohairpin or loop to permit the two elements to bind. The spacing betweentwo such hybridizing control elements can be as small as a t-RNA loop,to as large as 10 kb.

Typically, the spacing is no smaller than 5 bases; more typically, nosmaller than 8; more typically, no smaller than 15 bases; moretypically, no smaller than 20 bases; more typically, no smaller than 25bases; even more typically, no more than 30, 35, 40 or 50 bases.

Usually, the fragment size in no larger than 5 kb bases; more usually,no larger than 2 kb; more usually, no larger than 1 kb; more usually, nolarger than 800 bases; more usually, no larger than 500 bases; even moreusually, no more than 250, 200, 150 or 100 bases.

Such spacing between promoter control elements can be determined usingthe techniques and assays described above.

(4) Other Promoters

The following are promoters that are induced under stress conditions andcan be combined with those of the present invention: ldh1 (oxygenstress; tomato; see Germain and Ricard. 1997. Plant Mol Biol 35:949-54),GPx and CAT (oxygen stress; mouse; see Franco et al. 1999. Free RadicBiol Med 27:1122-32), ci7 (cold stress; potato; see Kirch et al. 1997.Plant Mol. Biol. 33:897-909), Bz2 (heavy metals; maize; see Marrs andWalbot. 1997. Plant Physiol 113:93-102), HSP32 (hyperthermia; rat; seeRaju and Maines. 1994. Biochim Biophys Acta 1217:273-80); MAPKAPK-2(heat shock; Drosophila; see Larochelle and Suter. 1995. Gene163:209-14).

In addition, the following examples of promoters are induced by thepresence or absence of light can be used in combination with those ofthe present invention: Topoisomerase II (pea; see Reddy et al. 1999.Plant Mol Biol 41:125-37), chalcone synthase (soybean; see Wingender etal. 1989. Mol Gen Genet 218:315-22) mdm2 gene (human tumor; see Saucedoet al. 1998. Cell Growth Differ 9:119-30), Clock and BMAL1 (rat; seeNamihira et al. 1999. Neurosci Lett 271:1-4, PHYA (Arabidopsis; seeCanton and Quail 1999. Plant Physiol 121:1207-16), PRB-1b (tobacco; seeSessa et al. 1995. Plant Mol Biol 28:537-47) and Ypr10 (common bean; seeWalter et al. 1996. Eur J Biochem 239:281-93).

The promoters and control elements of the following genes can be used incombination with the present invention to confer tissue specificity:MipB (iceplant; Yamada et al. 1995. Plant Cell 7:1129-42) and SUCS (rootnodules; broadbean; Kuster et al. 1993. Mol Plant Microbe Interact6:507-14) for roots, OsSUT1 (rice; Hirose et al. 1997. Plant CellPhysiol 38:1389-96) for leaves, Msg (soybean; Stomvik et al. 1999. PlantMol Biol 41:217-31) for siliques, cell (Arabidopsis; Shani et al. 1997.Plant Mol Biol 34(6):837-42) and ACT11 (Arabidopsis; Huang et al. 1997.Plant Mol Biol 33:125-39) for inflorescence.

Still other promoters are affected by hormones or participate inspecific physiological processes, which can be used in combination withthose of present invention. Some examples are the ACC synthase gene thatis induced differently by ethylene and brassinosteroids (mung bean; Yiet al. 1999. Plant Mol Biol 41:443-54), the TAPG1 gene that is activeduring abscission (tomato; Kalaitzis et al. 1995. Plant Mol Biol28:647-56), and the 1-aminocyclopropane-1-carboxylate synthase gene(carnation; Jones et al. 19951 Plant Mol Biol 28:505-12) and theCP-2/cathepsin L gene (rat; Kim and Wright. 1997. Biol Reprod57:1467-77), both active during senescence.

E. Vectors

Vectors are a useful component of the present invention. In particular,the present promoters and/or promoter control elements may be deliveredto a system such as a cell by way of a vector. For the purposes of thisinvention, such delivery may range from simply introducing the promoteror promoter control element by itself randomly into a cell tointegration of a cloning vector containing the present promoter orpromoter control element. Thus, a vector need not be limited to a DNAmolecule such as a plasmid, cosmid or bacterial phage that has thecapability of replicating autonomously in a host cell. All other mannerof delivery of the promoters and promoter control elements of theinvention are envisioned. The various T-DNA vector types are a preferredvector for use with the present invention. Many useful vectors arecommercially available.

It may also be useful to attach a marker sequence to the presentpromoter and promoter control element in order to determine activity ofsuch sequences. Marker sequences typically include genes that provideantibiotic resistance, such as tetracycline resistance, hygromycinresistance or ampicillin resistance, or provide herbicide resistance.Specific selectable marker genes may be used to confer resistance toherbicides such as glyphosate, glufosinate or broxynil (Comai et al.,Nature 317: 741-744 (1985); Gordon-Kamm et al., Plant Cell 2: 603-618(1990); and Stalker et al., Science 242: 419-423 (1988)). Other markergenes exist which provide hormone responsiveness.

(1) Modification of Transcription by Promoters and Promoter ControlElements

The promoter or promoter control element of the present invention may beoperably linked to a polynucleotide to be transcribed. In this manner,the promoter or promoter control element may modify transcription bymodulate transcript levels of that polynucleotide when inserted into agenome.

However, prior to insertion into a genome, the promoter or promotercontrol element need not be linked, operably or otherwise, to apolynucleotide to be transcribed. For example, the promoter or promotercontrol element may be inserted alone into the genome in front of apolynucleotide already present in the genome. In this manner, thepromoter or promoter control element may modulate the transcription of apolynucleotide that was already present in the genome. Thispolynucleotide may be native to the genome or inserted at an earliertime.

Alternatively, the promoter or promoter control element may be insertedinto a genome alone to modulate transcription. See, for example,Vaucheret, H et al. (1998) Plant J 16: 651-659. Rather, the promoter orpromoter control element may be simply inserted into a genome ormaintained extrachromosomally as a way to divert transcription resourcesof the system to itself. This approach may be used to downregulate thetranscript levels of a group of polynucleotide(s).

(2) Polynucleotide to be Transcribed

The nature of the polynucleotide to be transcribed is not limited.Specifically, the polynucleotide may include sequences that will haveactivity as RNA as well as sequences that result in a polypeptideproduct. These sequences may include, but are not limited to antisensesequences, ribozyme sequences, spliceosomes, amino acid codingsequences, and fragments thereof.

Specific coding sequences may include, but are not limited to endogenousproteins or fragments thereof, or heterologous proteins including markergenes or fragments thereof.

Promoters and control elements of the present invention are useful formodulating metabolic or catabolic processes. Such processes include, butare not limited to, secondary product metabolism, amino acid synthesis,seed protein storage, oil development, pest defense and nitrogen usage.Some examples of genes, transcripts and peptides or polypeptidesparticipating in these processes, which can be modulated by the presentinvention: are tryptophan decarboxylase (tdc) and strictosidine synthase(str1), dihydrodipicolinate synthase (DHDPS) and aspartate kinase (AK),2S albumin and alpha-, beta-, and gamma-zeins, ricinoleate and3-ketoacyl-ACP synthase (KAS), Bacillus thuringiensis (Bt) insecticidalprotein, cowpea trypsin inhibitor (CpTI), asparagine synthetase andnitrite reductase. Alternatively, expression constructs can be used toinhibit expression of these peptides and polypeptides by incorporatingthe promoters in constructs for antisense use, co-suppression use or forthe production of dominant negative mutations.

(3) Other Regulatory Elements

As explained above, several types of regulatory elements existconcerning transcription regulation. Each of these regulatory elementsmay be combined with the present vector if desired.

(4) Other Components of Vectors

Translation of eukaryotic mRNA is often initiated at the codon thatencodes the first methionine. Thus, when constructing a recombinantpolynucleotide according to the present invention for expressing aprotein product, it is preferable to ensure that the linkage between the3′ portion, preferably including the TATA box, of the promoter and thepolynucleotide to be transcribed, or a functional derivative thereof,does not contain any intervening codons which are capable of encoding amethionine.

The vector of the present invention may contain additional components.For example, an origin of replication allows for replication of thevector in a host cell. Additionally, homologous sequences flanking aspecific sequence allows for specific recombination of the specificsequence at a desired location in the target genome. T-DNA sequencesalso allow for insertion of a specific sequence randomly into a targetgenome.

The vector may also be provided with a plurality of restriction sitesfor insertion of a polynucleotide to be transcribed as well as thepromoter and/or promoter control elements of the present invention. Thevector may additionally contain selectable marker genes. The vector mayalso contain a transcriptional and translational initiation region, anda transcriptional and translational termination region functional in thehost cell. The termination region may be native with the transcriptionalinitiation region, may be native with the polynucleotide to betranscribed, or may be derived from another source. Convenienttermination regions are available from the Ti-plasmid of A. tumefaciens,such as the octopine synthase and nopaline synthase termination regions.See also, Guerineau et al., (1991) Mol. Gen. Genet. 262:141-144;Proudfoot (1991) Cell 64:671-674; Sanfacon et al. (1991) Genes Dev.5:141-149; Mogen et al. (1990) Plant Cell 2:1261-1272; Munroe et al.(1990) Gene 91:151-158; Ballas et al. 1989) Nucleic Acids Res.17:7891-7903; Joshi et al. (1987) Nucleic Acid Res. 15:9627-9639.

Where appropriate, the polynucleotide to be transcribed may be optimizedfor increased expression in a certain host cell. For example, thepolynucleotide can be synthesized using preferred codons for improvedtranscription and translation. See U.S. Pat. Nos. 5,380,831, 5,436,391;see also and Murray et al., (1989) Nucleic Acids Res. 17:477-498.

Additional sequence modifications include elimination of sequencesencoding spurious polyadenylation signals, exon intron splice sitesignals, transposon-like repeats, and other such sequences wellcharacterized as deleterious to expression. The G-C content of thepolynucleotide may be adjusted to levels average for a given cellularhost, as calculated by reference to known genes expressed in the hostcell. The polynucleotide sequence may be modified to avoid hairpinsecondary mRNA structures.

A general description of expression vectors and reporter genes can befound in Gruber, et al., “Vectors for Plant Transformation, in Methodsin Plant Molecular Biology & Biotechnology” in Glich et al., (Eds. pp.89-119, CRC Press, 1993). Moreover GUS expression vectors and GUS genecassettes are available from Clonetech Laboratories, Inc., Palo Alto,Calif. while luciferase expression vectors and luciferase gene cassettesare available from Promega Corp. (Madison, Wis.). GFP vectors areavailable from Aurora Biosciences.

F. Polynucleotide Insertion into a Host Cell

The polynucleotides according to the present invention can be insertedinto a host cell. A host cell includes but is not limited to a plant,mammalian, insect, yeast, and prokaryotic cell, preferably a plant cell.

The method of insertion into the host cell genome is chosen based onconvenience. For example, the insertion into the host cell genome mayeither be accomplished by vectors that integrate into the host cellgenome or by vectors which exist independent of the host cell genome.

(1) Polynucleotides Autonomous of the Host Genome

The polynucleotides of the present invention can exist autonomously orindependent of the host cell genome. Vectors of these types are known inthe art and include, for example, certain type of non-integrating viralvectors, autonomously replicating plasmids, artificial chromosomes, andthe like.

Additionally, in some cases transient expression of a polynucleotide maybe desired.

(2) Polynucleotides Integrated into the Host Genome

The promoter sequences, promoter control elements or vectors of thepresent invention may be transformed into host cells. Thesetransformations may be into protoplasts or intact tissues or isolatedcells. Preferably expression vectors are introduced into intact tissue.General methods of culturing plant tissues are provided for example byMaki et al. “Procedures for Introducing Foreign DNA into Plants” inMethods in Plant Molecular Biology & Biotechnology, Glich et al. (Eds.pp. 67-88 CRC Press, 1993); and by Phillips et al. “Cell-Tissue Cultureand In-Vitro Manipulation” in Corn & Corn Improvement, 3rd Edition10Sprague et al. (Eds. pp. 345-387) American Society of Agronomy Inc. etal. 1988.

Methods of introducing polynucleotides into plant tissue include thedirect infection or co-cultivation of plant cell with Agrobacteriumtumefaciens, Horsch et al., Science, 227:1229 (1985). Descriptions ofAgrobacterium vector systems and methods for Agrobacterium-mediated genetransfer provided by Gruber et al. supra.

Alternatively, polynucleotides are introduced into plant cells or otherplant tissues using a direct gene transfer method such asmicroprojectile-mediated delivery, DNA injection, electroporation andthe like. More preferably polynucleotides are introduced into planttissues using the microprojectile media delivery with the biolisticdevice. See, for example, Tomes et al., “Direct DNA transfer into intactplant cells via microprojectile bombardment” In: Gamborg and Phillips(Eds.) Plant Cell, Tissue and Organ Culture: Fundamental Methods,Springer Verlag, Berlin (1995).

In another embodiment of the current invention, expression constructscan be used for gene expression in callus culture for the purpose ofexpressing marker genes encoding peptides or polypeptides that allowidentification of transformed plants. Here, a promoter that isoperatively linked to a polynucleotide to be transcribed is transformedinto plant cells and the transformed tissue is then placed oncallus-inducing media. If the transformation is conducted with leafdiscs, for example, callus will initiate along the cut edges. Oncecallus growth has initiated, callus cells can be transferred to callusshoot-inducing or callus root-inducing media. Gene expression will occurin the callus cells developing on the appropriate media: callusroot-inducing promoters will be activated on callus root-inducing media,etc. Examples of such peptides or polypeptides useful as transformationmarkers include, but are not limited to barstar, glyphosate,chloramphenicol acetyltransferase (CAT), kanamycin, spectinomycin,streptomycin or other antibiotic resistance enzymes, green fluorescentprotein (GFP), and β-glucuronidase (GUS), etc. Some of the exemplarypromoters of the row titled “The predicted promoter sequence” will alsobe capable of sustaining expression in some tissues or organs after theinitiation or completion of regeneration. Examples of these tissues ororgans are somatic embryos, cotyledon, hypocotyl, epicotyl, leaf, stems,roots, flowers and seed.

Integration into the host cell genome also can be accomplished bymethods known in the art, for example, by the homologous sequences orT-DNA discussed above or using the cre-lox system (A. C. Vergunst etal., Plant Mol. Biol. 38:393 (1998)).

G. Utility

Common Uses

In yet another embodiment, the promoters of the present invention can beused to further understand developmental mechanisms. For example,promoters that are specifically induced during callus formation, somaticembryo formation, shoot formation or root formation can be used toexplore the effects of overexpression, repression or ectopic expressionof target genes, or for isolation of trans-acting factors.

The vectors of the invention can be used not only for expression ofcoding regions but may also be used in exon-trap cloning, or promotertrap procedures to detect differential gene expression in varioustissues, K. Lindsey et al., 1993 “Tagging Genomic Sequences That DirectTransgene Expression by Activation of a Promoter Trap in Plants”,Transgenic Research 2:3347. D. Auch & Reth, et al., “Exon Trap Cloning:Using PCR to Rapidly Detect and Clone Exons from Genomic DNA Fragments”,Nucleic Acids Research, Vol. 18, No. 22, p. 674.

Entrapment vectors, first described for use in bacteria (Casadaban andCohen, 1979, Proc. Nat. Aca. Sci. U.S.A., 76: 4530; Casadaban et al.,1980, J. Bacteriol., 143: 971) permit selection of insertional eventsthat lie within coding sequences. Entrapment vectors can be introducedinto pluripotent ES cells in culture and then passed into the germlinevia chimeras (Gossler et al., 1989, Science, 244: 463; Skarnes, 1990,Biotechnology, 8: 827). Promoter or gene trap vectors often contain areporter gene, e.g., lacZ, lacking its own promoter and/or spliceacceptor sequence upstream. That is, promoter gene traps contain areporter gene with a splice site but no promoter. If the vector lands ina gene and is spliced into the gene product, then the reporter gene isexpressed.

Recently, the isolation of preferentially-induced genes has been madepossible with the use of sophisticated promoter traps (e.g. IVET) thatare based on conditional auxotrophy complementation or drug resistance.In one IVET approach, various bacterial genome fragments are placed infront of a necessary metabolic gene coupled to a reporter gene. The DNAconstructs are inserted into a bacterial strain otherwise lacking themetabolic gene, and the resulting bacteria are used to infect the hostorganism. Only bacteria expressing the metabolic gene survive in thehost organism; consequently, inactive constructs can be eliminated byharvesting only bacteria that survive for some minimum period in thehost. At the same time, constitutively active constructs can beeliminated by screening only bacteria that do not express the reportergene under laboratory conditions. The bacteria selected by such a methodcontain constructs that are selectively induced only during infection ofthe host. The IVET approach can be modified for use in plants toidentify genes induced in either the bacteria or the plant cells uponpathogen infection or root colonization. For information on IVET see thearticles by Mahan et al. in Science 259:686-688 (1993), Mahan et al. inPNAS USA 92:669-673 (1995), Heithoff et al. in PNAS USA 94:934-939(1997), and Wang et al. in PNAS USA. 93:10434 (1996).

Constitutive Transcription

Use of promoters and control elements providing constitutivetranscription is desired for modulation of transcription in most cellsof an organism under most environmental conditions. In a plant, forexample, constitutive transcription is useful for modulating genesinvolved in defense, pest resistance, herbicide resistance, etc.

Constitutive up-regulation and transcription down-regulation is usefulfor these applications. For instance, genes, transcripts, and/orpolypeptides that increase defense, pest and herbicide resistance mayrequire constitutive up-regulation of transcription. In contrast,constitutive transcriptional down-regulation may be desired to inhibitthose genes, transcripts, and/or polypeptides that lower defense, pestand herbicide resistance.

Typically, promoter or control elements that provide constitutivetranscription produce transcription levels that are statisticallysimilar in many tissues and environmental conditions observed.

Calculation of P-value from the different observed transcript levels isone means of determining whether a promoter or control element isproviding constitutive up-regulation. P-value is the probability thatthe difference of transcript levels is not statistically significant.The higher the P-value, the more likely the difference of transcriptlevels is not significant. One formula used to calculate P-value is asfollows:∫φ(x)dx, integrated from a to ∞,

where φ(x) is a normal distribution;

$\mspace{11mu}{{{{where}\mspace{14mu} a} = \frac{{{Sx} - \mu}}{\sigma\left( {{all}{\mspace{11mu}\;}{Samples}\mspace{14mu}{except}\mspace{14mu}{Sx}} \right)}};}\mspace{14mu}$  where  Sx = the  intensity  of  the  sample   of  interest $\;\begin{matrix}{{{where}\mspace{14mu}\mu} = {{is}\mspace{14mu}{the}\mspace{14mu}{average}\mspace{14mu}{of}\mspace{14mu}{the}\mspace{14mu}{intensities}\mspace{14mu}{of}}} \\{{{{all}\mspace{14mu}{samples}\mspace{14mu}{except}\mspace{14mu}{Sx}},}\mspace{14mu}} \\{= \frac{\left( {\Sigma\; S\; 1\mspace{14mu}\ldots\mspace{14mu}{Sn}} \right) - {Sx}}{n - 1}}\end{matrix}$

where σ(S1 . . . S11, not including Sx)=the standard deviation of allsample intensities except Sx.

The P-value from the formula ranges from 1.0 to 0.0.

Usually, each P-value of the transcript levels observed in a majority ofcells, tissues, or organs under various environmental conditionsproduced by the promoter or control element is greater than 10⁻⁸; moreusually, greater than 10⁻⁷; even more usually, greater than 10⁻⁶; evenmore usually, greater than 10⁻⁵ or 10⁻⁴.

For up-regulation of transcription, promoter and control elementsproduce transcript levels that are above background of the assay.

Stress Induced Preferential Transcription

Promoters and control elements providing modulation of transcriptionunder oxidative, drought, oxygen, wound, and methyl jasmonate stress areparticularly useful for producing host cells or organisms that are moreresistant to biotic and abiotic stresses. In a plant, for example,modulation of genes, transcripts, and/or polypeptides in response tooxidative stress can protect cells against damage caused by oxidativeagents, such as hydrogen peroxide and other free radicals.

Drought induction of genes, transcripts, and/or polypeptides are usefulto increase the viability of a plant, for example, when water is alimiting factor. In contrast, genes, transcripts, and/or polypeptidesinduced during oxygen stress can help the flood tolerance of a plant.

The promoters and control elements of the present invention can modulatestresses similar to those described in, for example, stress conditionsare VuPLD1 (drought stress; Cowpea; see Pham-Thi et al. 1999. Plantmolecular Biology. 1257-65), pyruvate decarboxylase (oxygen stress;rice; see Rivosal et al. 1997. Plant Physiol. 114(3): 1021-29),chromoplast specific carotenoid gene (oxidative stress; capsicum; seeBouvier et al. 1998. Journal of Biological Chemistry 273: 30651-59).

Promoters and control elements providing preferential transcriptionduring wounding or induced by methyl jasmonate can produce a defenseresponse in host cells or organisms. In a plant, for example,preferential modulation of genes, transcripts, and/or polypeptides undersuch conditions is useful to induce a defense response to mechanicalwounding, pest or pathogen attack or treatment with certain chemicals.

Promoters and control elements of the present invention also can triggera response similar to those described for cf9 (viral pathogen; tomato;see O'Donnell et al. 1998. The Plant journal: for cell and molecularbiology 14(1): 137-42), hepatocyte growth factor activator inhibitortype 1 (HAI-1), which enhances tissue regeneration (tissue injury;human; Koono et al. 1999. Journal of Histochemistry and Cytochemistry47: 673-82), copper amine oxidase (CuAO), induced during ontogenesis andwound healing (wounding; chick-pea; Rea et al. 1998. FEBS Letters 437:177-82), proteinase inhibitor II (wounding; potato; see Pena-Cortes etal. 1988. Planta 174: 84-89), protease inhibitor II (methyl jasmonate;tomato; see Farmer and Ryan. 1990. Proc Natl Acad Sci USA 87:7713-7716), two vegetative storage protein genes VspA and VspB(wounding, jasmonic acid, and water deficit; soybean; see Mason andMullet. 1990. Plant Cell 2: 569-579).

Up-regulation and transcription down-regulation are useful for theseapplications. For instance, genes, transcripts, and/or polypeptides thatincrease oxidative, flood, or drought tolerance may requireup-regulation of transcription. In contrast, transcriptionaldown-regulation may be desired to inhibit those genes, transcripts,and/or polypeptides that lower such tolerance.

Typically, promoter or control elements, which provide preferentialtranscription in wounding or under methyl jasmonate induction, producetranscript levels that are statistically significant as compared to celltypes, organs or tissues under other conditions.

For preferential up-regulation of transcription, promoter and controlelements produce transcript levels that are above background of theassay.

Light Induced Preferential Transcription

Promoters and control elements providing preferential transcription wheninduced by light exposure can be utilized to modulate growth,metabolism, and development; to increase drought tolerance; and decreasedamage from light stress for host cells or organisms. In a plant, forexample, modulation of genes, transcripts, and/or polypeptides inresponse to light is useful

-   -   (1) to increase the photosynthetic rate;    -   (2) to increase storage of certain molecules in leaves or green        parts only, e.g., silage with high protein or starch content;    -   (3) to modulate production of exogenous compositions in green        tissue, e.g., certain feed enzymes;    -   (4) to induce growth or development, such as fruit development        and maturity, during extended exposure to light;    -   (5) to modulate guard cells to control the size of stomata in        leaves to prevent water loss, or    -   (6) to induce accumulation of beta-carotene to help plants cope        with light induced stress.        The promoters and control elements of the present invention also        can trigger responses similar to those described in: abscisic        acid insensitive3 (ABI3) (dark-grown Arabidopsis seedlings, see        Rohde et al. 2000. The Plant Cell 12: 35-52), asparagine        synthetase (pea root nodules, see Tsai, F. Y.;        Coruzzi, G. M. 1990. EMBO J 9: 323-32), mdm2 gene (human tumor;        see Saucedo et al. 1998. Cell Growth Differ 9: 119-30).

Up-regulation and transcription down-regulation are useful for theseapplications. For instance, genes, transcripts, and/or polypeptides thatincrease drought or light tolerance may require up-regulation oftranscription. In contrast, transcriptional down-regulation may bedesired to inhibit those genes, transcripts, and/or polypeptides thatlower such tolerance.

Typically, promoter or control elements, which provide preferentialtranscription in cells, tissues or organs exposed to light, producetranscript levels that are statistically significant as compared tocells, tissues, or organs under decreased light exposure (intensity orlength of time).

For preferential up-regulation of transcription, promoter and controlelements produce transcript levels that are above background of theassay.

Dark Induced Preferential Transcription

Promoters and control elements providing preferential transcription wheninduced by dark or decreased light intensity or decreased light exposuretime can be utilized to time growth, metabolism, and development, tomodulate photosynthesis capabilities for host cells or organisms. In aplant, for example, modulation of genes, transcripts, and/orpolypeptides in response to dark is useful, for example,

-   -   (1) to induce growth or development, such as fruit development        and maturity, despite lack of light;    -   (2) to modulate genes, transcripts, and/or polypeptide active at        night or on cloudy days; or    -   (3) to preserve the plastid ultra structure present at the onset        of darkness.        The present promoters and control elements can also trigger        response similar to those described in the section above.

Up-regulation and transcription down-regulation is useful for theseapplications. For instance, genes, transcripts, and/or polypeptides thatincrease growth and development may require up-regulation oftranscription. In contrast, transcriptional down-regulation may bedesired to inhibit those genes, transcripts, and/or polypeptides thatmodulate photosynthesis capabilities.

Typically, promoter or control elements, which provide preferentialtranscription under exposure to dark or decrease light intensity ordecrease exposure time, produce transcript levels that are statisticallysignificant.

For preferential up-regulation of transcription, promoter and controlelements produce transcript levels that are above background of theassay.

Leaf Preferential Transcription

Promoters and control elements providing preferential transcription in aleaf can modulate growth, metabolism, and development or modulate energyand nutrient utilization in host cells or organisms. In a plant, forexample, preferential modulation of genes, transcripts, and/orpolypeptide in a leaf, is useful, for example,

(1) to modulate leaf size, shape, and development;

(2) to modulate the number of leaves; or

(3) to modulate energy or nutrient usage in relation to other organs andtissues

Up-regulation and transcription down-regulation is useful for theseapplications. For instance, genes, transcripts, and/or polypeptides thatincrease growth, for example, may require up-regulation oftranscription. In contrast, transcriptional down-regulation may bedesired to inhibit energy usage in a leaf to be directed to the fruitinstead, for instance.

Typically, promoter or control elements, which provide preferentialtranscription in the cells, tissues, or organs of a leaf, producetranscript levels that are statistically significant as compared toother cells, organs or tissues.

For preferential up-regulation of transcription, promoter and controlelements produce transcript levels that are above background of theassay.

Root Preferential Transcription

Promoters and control elements providing preferential transcription in aroot can modulate growth, metabolism, development, nutrient uptake,nitrogen fixation, or modulate energy and nutrient utilization in hostcells or organisms. In a plant, for example, preferential modulation ofgenes, transcripts, and/or in a leaf, is useful

(1) to modulate root size, shape, and development;

(2) to modulate the number of roots, or root hairs;

(3) to modulate mineral, fertilizer, or water uptake;

(4) to modulate transport of nutrients; or

(4) to modulate energy or nutrient usage in relation to other organs andtissues.

Up-regulation and transcription down-regulation is useful for theseapplications. For instance, genes, transcripts, and/or polypeptides thatincrease growth, for example, may require up-regulation oftranscription. In contrast, transcriptional down-regulation may bedesired to inhibit nutrient usage in a root to be directed to the leafinstead, for instance.

Typically, promoter or control elements, which provide preferentialtranscription in cells, tissues, or organs of a root, produce transcriptlevels that are statistically significant as compared to other cells,organs or tissues.

For preferential up-regulation of transcription, promoter and controlelements produce transcript levels that are above background of theassay.

Stem/Shoot Preferential Transcription

Promoters and control elements providing preferential transcription in astem or shoot can modulate growth, metabolism, and development ormodulate energy and nutrient utilization in host cells or organisms. Ina plant, for example, preferential modulation of genes, transcripts,and/or polypeptide in a stem or shoot, is useful, for example,

(1) to modulate stem/shoot size, shape, and development; or

(2) to modulate energy or nutrient usage in relation to other organs andtissues

Up-regulation and transcription down-regulation is useful for theseapplications. For instance, genes, transcripts, and/or polypeptides thatincrease growth, for example, may require up-regulation oftranscription. In contrast, transcriptional down-regulation may bedesired to inhibit energy usage in a stem/shoot to be directed to thefruit instead, for instance.

Typically, promoter or control elements, which provide preferentialtranscription in the cells, tissues, or organs of a stem or shoot,produce transcript levels that are statistically significant as comparedto other cells, organs or tissues.

-   -   For preferential up-regulation of transcription, promoter and        control elements produce transcript levels that are above        background of the assay.

Fruit and Seed Preferential Transcription

Promoters and control elements providing preferential transcription in asilique or fruit can time growth, development, or maturity; or modulatefertility; or modulate energy and nutrient utilization in host cells ororganisms. In a plant, for example, preferential modulation of genes,transcripts, and/or polypeptides in a fruit, is useful

-   -   (1) to modulate fruit size, shape, development, and maturity;    -   (2) to modulate the number of fruit or seeds;    -   (3) to modulate seed shattering;    -   (4) to modulate components of seeds, such as, storage molecules,        starch, protein, oil, vitamins, anti-nutritional components,        such as phytic acid;    -   (5) to modulate seed and/or seedling vigor or viability;    -   (6) to incorporate exogenous compositions into a seed, such as        lysine rich proteins;    -   (7) to permit similar fruit maturity timing for early and late        blooming flowers; or    -   (8) to modulate energy or nutrient usage in relation to other        organs and tissues.

Up-regulation and transcription down-regulation is useful for theseapplications. For instance, genes, transcripts, and/or polypeptides thatincrease growth, for example, may require up-regulation oftranscription. In contrast, transcriptional down-regulation may bedesired to inhibit late fruit maturity, for instance.

Typically, promoter or control elements, which provide preferentialtranscription in the cells, tissues, or organs of siliques or fruits,produce transcript levels that are statistically significant as comparedto other cells, organs or tissues.

For preferential up-regulation of transcription, promoter and controlelements produce transcript levels that are above background of theassay.

Callus Preferential Transcription

Promoters and control elements providing preferential transcription in acallus can be useful to modulating transcription in dedifferentiatedhost cells. In a plant transformation, for example, preferentialmodulation of genes, transcripts, in callus is useful to modulatetranscription of a marker gene, which can facilitate selection of cellsthat are transformed with exogenous polynucleotides.

Up-regulation and transcription down-regulation is useful for theseapplications. For instance, genes, transcripts, and/or polypeptides thatincrease marker gene detectability, for example, may requireup-regulation of transcription. In contrast, transcriptionaldown-regulation may be desired to increase the ability of the callusesto later differentiate, for instance.

Typically, promoter or control elements, which provide preferentialtranscription in callus, produce transcript levels that arestatistically significant as compared to other cell types, tissues, ororgans. Calculation of P-value from the different observed transcriptlevels is one means of determining whether a promoter or control elementis providing such preferential transcription.

Usually, each P-value of the transcript levels observed in callus ascompared to, at least one other cell type, tissue or organ, is less than10⁻⁴; more usually, less than 10⁻⁵; even more usually, less than 10⁻⁶;even more usually, less than 10⁻⁷ or 10⁻⁸.

For preferential up-regulation of transcription, promoter and controlelements produce transcript levels that are above background of theassay.

Flower Specific Transcription

Promoters and control elements providing preferential transcription inflowers can modulate pigmentation; or modulate fertility in host cellsor organisms. In a plant, for example, preferential modulation of genes,transcripts, and/or polypeptides in a flower, is useful,

(1) to modulate petal color; or

(2) to modulate the fertility of pistil and/or stamen.

Up-regulation and transcription down-regulation is useful for theseapplications. For instance, genes, transcripts, and/or polypeptides thatincrease pigmentation, for example, may require up-regulation oftranscription. In contrast, transcriptional down-regulation may bedesired to inhibit fertility, for instance.

Typically, promoter or control elements, which provide preferentialtranscription in flowers, produce transcript levels that arestatistically significant as compared to other cells, organs or tissues.

For preferential up-regulation of transcription, promoter and controlelements produce transcript levels that are above background of theassay.

Immature Bud and Inflorescence Preferential Transcription

Promoters and control elements providing preferential transcription in aimmature bud or inflorescence can time growth, development, or maturity;or modulate fertility or viability in host cells or organisms. In aplant, for example, preferential modulation of genes, transcripts,and/or polypeptide in a fruit, is useful,

(1) to modulate embryo development, size, and maturity;

(2) to modulate endosperm development, size, and composition;

(3) to modulate the number of seeds and fruits; or

(4) to modulate seed development and viability.

Up-regulation and transcription down-regulation is useful for theseapplications. For instance, genes, transcripts, and/or polypeptides thatincrease growth, for example, may require up-regulation oftranscription. In contrast, transcriptional down-regulation may bedesired to decrease endosperm size, for instance.

Typically, promoter or control elements, which provide preferentialtranscription in immature buds and inflorescences, produce transcriptlevels that are statistically significant as compared to other celltypes, organs or tissues.

For preferential up-regulation of transcription, promoter and controlelements produce transcript levels that are above background of theassay.

Senescence Preferential Transcription

Promoters and control elements providing preferential transcriptionduring senescence can be used to modulate cell degeneration, nutrientmobilization, and scavenging of free radicals in host cells ororganisms. Other types of responses that can be modulated include, forexample, senescence associated genes (SAG) that encode enzymes thoughtto be involved in cell degeneration and nutrient mobilization(Arabidopsis; see Hensel et al. 1993. Plant Cell 5: 553-64), and theCP-2/cathepsin L gene (rat; Kim and Wright. 1997. Biol Reprod 57:1467-77), both induced during senescence.

In a plant, for example, preferential modulation of genes, transcripts,and/or polypeptides during senescencing is useful to modulate fruitripening.

Up-regulation and transcription down-regulation is useful for theseapplications. For instance, genes, transcripts, and/or polypeptides thatincrease scavenging of free radicals, for example, may requireup-regulation of transcription. In contrast, transcriptionaldown-regulation may be desired to inhibit cell degeneration, forinstance.

Typically, promoter or control elements, which provide preferentialtranscription in cells, tissues, or organs during senescence, producetranscript levels that are statistically significant as compared toother conditions.

For preferential up-regulation of transcription, promoter and controlelements produce transcript levels that are above background of theassay.

Germination Preferential Transcription

Promoters and control elements providing preferential transcription in agerminating seed can time growth, development, or maturity; or modulateviability in host cells or organisms. In a plant, for example,preferential modulation of genes, transcripts, and/or polypeptide in agerminating seed, is useful,

(1) to modulate the emergence of they hypocotyls, cotyledons andradical; or

(2) to modulate shoot and primary root growth and development;

Up-regulation and transcription down-regulation is useful for theseapplications. For instance, genes, transcripts, and/or polypeptides thatincrease growth, for example, may require up-regulation oftranscription. In contrast, transcriptional down-regulation may bedesired to decrease endosperm size, for instance.

Typically, promoter or control elements, which provide preferentialtranscription in a germinating seed, produce transcript levels that arestatistically significant as compared to other cell types, organs ortissues.

For preferential up-regulation of transcription, promoter and controlelements produce transcript levels that are above background of theassay.

Microarray Analysis

A major way that a cell controls its response to internal or externalstimuli is by regulating the rate of transcription of specific genes.For example, the differentiation of cells during organogenensis intoforms characteristic of the organ is associated with the selectiveactivation and repression of large numbers of genes. Thus, specificorgans, tissues and cells are functionally distinct due to the differentpopulations of mRNAs and protein products they possess. Internal signalsprogram the selective activation and repression programs. For example,internally synthesized hormones produce such signals. The level ofhormone can be raised by increasing the level of transcription of genesencoding proteins concerned with hormone synthesis.

To measure how a cell reacts to internal and/or external stimuli,individual mRNA levels can be measured and used as an indicator for theextent of transcription of the gene. Cells can be exposed to a stimulus,and mRNA can be isolated and assayed at different time points afterstimulation. The mRNA from the stimulated cells can be compared tocontrol cells that were not stimulated. The mRNA levels that are higherin the stimulated cell versus the control indicate a stimulus-specificresponse of the cell. The same is true of mRNA levels that are lower instimulated cells versus the control condition.

Similar studies can be performed with cells taken from an organism witha defined mutation in their genome as compared with cells without themutation. Altered mRNA levels in the mutated cells indicate how themutation causes transcriptional changes. These transcriptional changesare associated with the phenotype that the mutated cells exhibit that isdifferent from the phenotype exhibited by the control cells.

Applicants have utilized microarray techniques to measure the levels ofmRNAs in cells from plants transformed with a construct containing thepromoter or control elements of the present invention together withtheir endogenous cDNA sequences. In general, transformants with theconstructs were grown to an appropriate stage, and tissue samples wereprepared for the microarray differential expression analysis. In thismanner it is possible to determine the differential expression for thecDNAs under the control of the endogenous promoter under variousconditions.

Microarray Experimental Procedures and Results

Procedures

1. Sample Tissue Preparation

Tissue samples for each of the expression analysis experiments wereprepared as follows:

(a) Roots

Seeds of Arabidopsis thaliana (Ws) were sterilized in full strengthbleach for less than 5 min., washed more than 3 times in steriledistilled deionized water and plated on MS agar plates. The plates wereplaced at 4° C. for 3 nights and then placed vertically into a growthchamber having 16 hr light/8 hr dark cycles, 23° C., 70% relativehumidity and ˜11,000 LUX. After 2 weeks, the roots were cut from theagar, flash frozen in liquid nitrogen and stored at −80° C.

(b) Rosette Leaves, Stems, and Siliques

Arabidopsis thaliana (Ws) seed was vernalized at 4° C. for 3 days beforesowing in Metro-mix soil type 350. Flats were placed in a growth chamberhaving 16 hr light/8 hr dark, 80% relative humidity, 23° C. and 13,000LUX for germination and growth. After 3 weeks, rosette leaves, stems,and siliques were harvested, flash frozen in liquid nitrogen and storedat −80° C. until use. After 4 weeks, siliques (<5 mm, 5-10 mm and >10mm) were harvested, flash frozen in liquid nitrogen and stored at −80°C. until use. 5 week old whole plants (used as controls) were harvested,flash frozen in liquid nitrogen and kept at −80° C. until RNA wasisolated.

(c) Germination

Arabidopsis thaliana seeds (ecotype Ws) were sterilized in bleach andrinsed with sterile water. The seeds were placed in 100 mm petri platescontaining soaked autoclaved filter paper. Plates were foil-wrapped andleft at 4° C. for 3 nights to vernalize. After cold treatment, the foilwas removed and plates were placed into a growth chamber having 16 hrlight/8 hr dark cycles, 23° C., 70% relative humidity and ˜11,000 lux.Seeds were collected 1 d, 2 d, 3 d and 4 d later, flash frozen in liquidnitrogen and stored at −80° C. until RNA was isolated.

(d) Abscissic Acid (ABA)

Seeds of Arabidopsis thaliana (ecotype Wassilewskija) were sown in traysand left at 4° C. for 4 days to vernalize. They were then transferred toa growth chamber having grown 16 hr light/8 hr dark, 13,000 LUX, 70%humidity, and 20° C. and watered twice a week with 1 L of 1× Hoagland'ssolution. Approximately 1,000 14 day old plants were spayed with 200-250mls of 100 μM ABA in a 0.02% solution of the detergent Silwet L-77.Whole seedlings, including roots, were harvested within a 15 to 20minute time period at 1 hr and 6 hr after treatment, flash-frozen inliquid nitrogen and stored at −80° C.

Seeds of maize hybrid 35A (Pioneer) were sown in water-moistened sand inflats (10 rows, 5-6 seed/row) and covered with clear, plastic lidsbefore being placed in a growth chamber having 16 hr light (25° C.)/8 hrdark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Coveredflats were watered every three days for 7 days. Seedlings were carefullyremoved from the sand and placed in 1-liter beakers with 100 μM ABA fortreatment. Control plants were treated with water. After 6 hr and 24 hr,aerial and root tissues were separated and flash frozen in liquidnitrogen prior to storage at −80° C.

(e) Brassinosteroid Responsive

Two separate experiments were performed, one with epi-brassinolide andone with the brassinosteroid biosynthetic inhibitor brassinazole. In theepi-brassinolide experiments, seeds of wild-type Arabidopsis thaliana(ecotype Wassilewskija) and the brassinosteroid biosynthetic mutantdwf4-1 were sown in trays and left at 4° C. for 4 days to vernalize.They were then transferred to a growth chamber having 16 hr light/8 hrdark, 11,000 LUX, 70% humidity and 22° C. temperature. Four week oldplants were spayed with a 1 μM solution of epi-brassinolide and shootparts (unopened floral primordia and shoot apical meristems) harvestedthree hours later. Tissue was flash-frozen in liquid nitrogen and storedat −80° C. In the brassinazole experiments, seeds of wild-typeArabidopsis thaliana (ecotype Wassilewskija) were grown as describedabove. Four week old plants were spayed with a 1 μM solution ofbrassinazole and shoot parts (unopened floral primordia and shoot apicalmeristems) harvested three hours later. Tissue was flash-frozen inliquid nitrogen and stored at −80° C.

In addition to the spray experiments, tissue was prepared from twodifferent mutants; (1) a dwf4-1 knock out mutant and (2) a mutantoverexpressing the dwf4-1 gene.

Seeds of wild-type Arabidopsis thaliana (ecotype Wassilewskija) and ofthe dwf4-1 knock out and overexpressor mutants were sown in trays andleft at 4° C. for 4 days to vernalize. They were then transferred to agrowth chamber having 16 hr light/8 hr dark, 11,000 LUX, 70% humidityand 22° C. temperature. Tissue from shoot parts (unopened floralprimordia and shoot apical meristems) was flash-frozen in liquidnitrogen and stored at −80° C.

Another experiment was completed with seeds of Arabidopsis thaliana(ecotype Wassilewskija) were sown in trays and left at 4° C. for 4 daysto vernalize. They were then transferred to a growth chamber. Plantswere grown under long-day (16 hr light: 8 hr. dark) conditions, 13,000LUX light intensity, 70% humidity, 20° C. temperature and watered twicea week with 1 L 1× Hoagland's solution (recipe recited in Feldmann etal., (1987) Mol. Gen. Genet. 208: 1-9 and described as complete nutrientsolution). Approximately 1,000 14 day old plants were spayed with200-250 mls of 0.1 μM Epi-Brassinolite in 0.02% solution of thedetergent Silwet L-77. At 1 hr. and 6 hrs. after treatment aerialtissues were harvested within a 15 to 20 minute time period andflash-frozen in liquid nitrogen.

Seeds of maize hybrid 35A (Pioneer) were sown in water-moistened sand inflats (10 rows, 5-6 seed/row) and covered with clear, plastic lidsbefore being placed in a growth chamber having 16 hr light (25° C.)/8 hrdark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Coveredflats were watered every three days for 7 days. Seedlings were carefullyremoved from the sand and placed in 1-liter beakers with 0.1 μMepi-brassinolide for treatment. Control plants were treated withdistilled deionized water. After 24 hr, aerial and root tissues wereseparated and flash frozen in liquid nitrogen prior to storage at −80°C.

(f) Nitrogen: High to Low

Wild type Arabidopsis thaliana seeds (ecotpye Ws) were surfacesterilized with 30% Clorox, 0.1% Triton X-100 for 5 minutes. Seeds werethen rinsed with 4-5 exchanges of sterile double distilled deionizedwater. Seeds were vernalized at 4° C. for 2-4 days in darkness. Aftercold treatment, seeds were plated on modified 1×MS media (without NH₄NO₃or KNO₃), 0.5% sucrose, 0.5 g/L MES pH5.7, 1% phytagar and supplementedwith KNO₃ to a final concentration of 60 mM (high nitrate modified 1×MSmedia). Plates were then grown for 7 days in a Percival growth chamberat 22° C. with 16 hr. light/8 hr dark.

Germinated seedlings were then transferred to a sterile flask containing50 mL of high nitrate modified 1×MS liquid media. Seedlings were grownwith mild shaking for 3 additional days at 22° C. in 16 hr. light/8 hrdark (in a Percival growth chamber) on the high nitrate modified 1×MSliquid media.

After three days of growth on high nitrate modified 1×MS liquid media,seedlings were transferred either to a new sterile flask containing 50mL of high nitrate modified 1×MS liquid media or to low nitrate modified1×MS liquid media (containing 20 □M KNO₃). Seedlings were grown in thesemedia conditions with mild shaking at 22° C. in 16 hr light/8 hr darkfor the appropriate time points and whole seedlings harvested for totalRNA isolation via the Trizol method (LifeTech.). The time points usedfor the microarray experiments were 10 min. and 1 hour time points forboth the high and low nitrate modified 1×MS media.

Alternatively, seeds that were surface sterilized in 30% bleachcontaining 0.1% Triton X-100 and further rinsed in sterile water, wereplanted on MS agar, (0.5% sucrose) plates containing 50 mM KNO₃(potassium nitrate). The seedlings were grown under constant light (3500LUX) at 22° C. After 12 days, seedlings were transferred to MS agarplates containing either 1 mM KNO₃ or 50 mM KNO₃. Seedlings transferredto agar plates containing 50 mM KNO₃ were treated as controls in theexperiment. Seedlings transferred to plates with 1 mM KNO₃ were rinsedthoroughly with sterile MS solution containing 1 mM KNO₃. There were tenplates per transfer. Root tissue was collected and frozen in 15 mLFalcon tubes at various time points which included 1 hour, 2 hours, 3hours, 4 hours, 6 hours, 9 hours, 12 hours, 16 hours, and 24 hours.

Maize 35A19 Pioneer hybrid seeds were sown on flats containing sand andgrown in a Conviron growth chamber at 25° C., 16 hr light/8 hr dark,˜13,000 LUX and 80% relative humidity. Plants were watered every threedays with double distilled deionized water. Germinated seedlings areallowed to grow for 10 days and were watered with high nitrate modified1×MS liquid media (see above). On day 11, young corn seedlings wereremoved from the sand (with their roots intact) and rinsed briefly inhigh nitrate modified 1×MS liquid media. The equivalent of half a flatof seedlings were then submerged (up to their roots) in a beakercontaining either 500 mL of high or low nitrate modified 1×MS liquidmedia (see above for details).

At appropriate time points, seedlings were removed from their respectiveliquid media, the roots separated from the shoots and each tissue typeflash frozen in liquid nitrogen and stored at −80° C. This was repeatedfor each time point. Total RNA was isolated using the Trizol method (seeabove) with root tissues only.

Corn root tissues isolated at the 4 hr and 16 hr time points were usedfor the microarray experiments. Both the high and low nitrate modified1×MS media were used.

(g) Nitrogen: Low to High

Arabidopsis thaliana ecotype Ws seeds were sown on flats containing 4 Lof a 1:2 mixture of Grace Zonolite vermiculite and soil. Flats werewatered with 3 L of water and vernalized at 4° C. for five days. Flatswere placed in a Conviron growth chamber having 16 hr light/8 hr dark at20° C., 80% humidity and 17.450 LUX. Flats were watered withapproximately 1.5 L of water every four days. Mature, bolting plants (24days after germination) were bottom treated with 2 L of either a control(100 mM mannitol pH 5.5) or an experimental (50 mM ammonium nitrate, pH5.5) solution. Roots, leaves and siliques were harvested separately 30,120 and 240 minutes after treatment, flash frozen in liquid nitrogen andstored at −80° C.

Hybrid maize seed (Pioneer hybrid 35A19) were aerated overnight indeionized water. Thirty seeds were plated in each flat, which contained4 liters of Grace zonolite vermiculite. Two liters of water were bottomfed and flats were kept in a Conviron growth chamber with 16 hr light/8hr dark at 20° C. and 80% humidity. Flats were watered with 1 L of tapwater every three days. Five day old seedlings were treated as describedabove with 2 L of either a control (100 mM mannitol pH 6.5) solution or1 L of an experimental (50 mM ammonium nitrate, pH 6.8) solution.Fifteen shoots per time point per treatment were harvested 10, 90 and180 minutes after treatment, flash frozen in liquid nitrogen and storedat −80° C.

Alternatively, seeds of Arabidopsis thaliana (ecotype Wassilewskija)were left at 4° C. for 3 days to vernalize. They were then sown onvermiculite in a growth chamber having 16 hours light/8 hours dark,12,000-14,000 LUX, 70% humidity, and 20° C. They were bottom-wateredwith tap water, twice weekly. Twenty-four days old plants were sprayedwith either water (control) or 0.6% ammonium nitrate at 4 μL/cm² of traysurface. Total shoots and some primary roots were cleaned ofvermiculite, flash-frozen in liquid nitrogen and stored at −80° C.

(h) Methyl Jasmonate

Seeds of Arabidopsis thaliana (ecotype Wassilewskija) were sown in traysand left at 4° C. for 4 days to vernalize before being transferred to agrowth chamber having 16 hr light/8 hr. dark, 13,000 LUX, 70% humidity,20° C. temperature and watered twice a week with 1 L of a 1× Hoagland'ssolution. Approximately 1,000 14 day old plants were spayed with 200-250mls of 0.001% methyl jasmonate in a 0.02% solution of the detergentSilwet L-77. At 1 hr and 6 hrs after treatment, whole seedlings,including roots, were harvested within a 15 to 20 minute time period,flash-frozen in liquid nitrogen and stored at −80° C.

Seeds of maize hybrid 35A (Pioneer) were sown in water-moistened sand inflats (10 rows, 5-6 seed/row) and covered with clear, plastic lidsbefore being placed in a growth chamber having 16 hr light (25° C.)/8 hrdark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Coveredflats were watered every three days for 7 days. Seedlings were carefullyremoved from the sand and placed in 1-liter beakers with 0.001% methyljasmonate for treatment. Control plants were treated with water. After24 hr, aerial and root tissues were separated and flash frozen in liquidnitrogen prior to storage at −80° C.

(i) Salicylic Acid

Seeds of Arabidopsis thaliana (ecotype Wassilewskija) were sown in traysand left at 4° C. for 4 days to vernalize before being transferred to agrowth chamber having 16 hr light/8 hr. dark, 13,000 LUX, 70% humidity,20° C. temperature and watered twice a week with 1 L of a 1× Hoagland'ssolution. Approximately 1,000 14 day old plants were spayed with 200-250mls of 5 mM salicylic acid (solubilized in 70% ethanol) in a 0.02%solution of the detergent Silwet L-77. At 1 hr and 6 hrs aftertreatment, whole seedlings, including roots, were harvested within a 15to 20 minute time period flash-frozen in liquid nitrogen and stored at−80° C.

Alternatively, seeds of wild-type Arabidopsis thaliana (ecotypeColumbia) and mutant CS3726 were sown in soil type 200 mixed withosmocote fertilizer and Marathon insecticide and left at 4° C. for 3days to vernalize. Flats were incubated at room temperature withcontinuous light. Sixteen days post germination plants were sprayed with2 mM SA, 0.02% SilwettL-77 or control solution (0.02% SilwettL-77.Aerial parts or flowers were harvested 1 hr, 4 hr, 6 hr, 24 hr and 3weeks post-treatment flash frozen and stored at −80° C.

Seeds of maize hybrid 35A (Pioneer) were sown in water-moistened sand inflats (10 rows, 5-6 seed/row) and covered with clear, plastic lidsbefore being placed in a growth chamber having 16 hr light (25° C.)/8 hrdark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Coveredflats were watered every three days for 7 days. Seedlings were carefullyremoved from the sand and placed in 1-liter beakers with 2 mM SA fortreatment. Control plants were treated with water. After 12 hr and 24hr, aerial and root tissues were separated and flash frozen in liquidnitrogen prior to storage at −80° C.

(j) Drought Stress

Seeds of Arabidopsis thaliana (Wassilewskija) were sown in pots and leftat 4° C. for three days to vernalize before being transferred to agrowth chamber having 16 hr light/8 hr dark, 150,000-160,000 LUX, 20° C.and 70% humidity. After 14 days, aerial tissues were cut and left to dryon 3 MM Whatman paper in a Petri-plate for 1 hour and 6 hours. Aerialtissues exposed for 1 hour and 6 hours to 3 MM Whatman paper wetted with1× Hoagland's solution served as controls. Tissues were harvested,flash-frozen in liquid nitrogen and stored at −80° C.

Alternatively, Arabidopsis thaliana (Ws) seed was vernalized at 4° C.for 3 days before sowing in Metromix soil type 350. Flats were placed ina growth chamber with 23° C., 16 hr light/8 hr. dark, 80% relativehumidity, ˜13,000 LUX for germination and growth. Plants were wateredwith 1-1.5 L of water every four days. Watering was stopped 16 daysafter germination for the treated samples, but continued for the controlsamples. Rosette leaves and stems, flowers and siliques were harvested 2d, 3 d, 4 d, 5 d, 6 d and 7 d after watering was stopped. Tissue wasflash frozen in liquid nitrogen and kept at −80° C. until RNA wasisolated. Flowers and siliques were also harvested on day 8 from plantsthat had undergone a 7 d drought treatment followed by 1 day ofwatering. Control plants (whole plants) were harvested after 5 weeks,flash frozen in liquid nitrogen and stored as above.

Seeds of maize hybrid 35A (Pioneer) were sown in water-moistened sand inflats (10 rows, 5-6 seed/row) and covered with clear, plastic lidsbefore being placed in a growth chamber having 16 hr light (25° C.)/8 hrdark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Coveredflats were watered every three days for 7 days. Seedlings were carefullyremoved from the sand and placed in empty 1-liter beakers at roomtemperature for treatment. Control plants were placed in water. After 1hr, 6 hr, 12 hr and 24 hr aerial and root tissues were separated andflash frozen in liquid nitrogen prior to storage at −80° C.

(k) Osmotic Stress

Seeds of Arabidopsis thaliana (Wassilewskija) were sown in trays andleft at 4° C. for three days to vernalize before being transferred to agrowth chamber having 16 hr light/8 hr dark, 12,000-14,000 LUX, 20° C.,and 70% humidity. After 14 days, the aerial tissues were cut and placedon 3 MM Whatman paper in a petri-plate wetted with 20% PEG (polyethyleneglycol-M_(r) 8,000) in 1× Hoagland's solution. Aerial tissues on 3 MMWhatman paper containing 1× Hoagland's solution alone served as thecontrol. Aerial tissues were harvested at 1 hour and 6 hours aftertreatment, flash-frozen in liquid nitrogen and stored at −80° C.

Seeds of maize hybrid 35A (Pioneer) were sown in water-moistened sand inflats (10 rows, 5-6 seed/row) and covered with clear, plastic lidsbefore being placed in a growth chamber having 16 hr light (25° C.)/8 hrdark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Coveredflats were watered every three days for 7 days. Seedlings were carefullyremoved from the sand and placed in 1-liter beakers with 10% PEG(polyethylene glycol-M_(r) 8,000) for treatment. Control plants weretreated with water. After 1 hr and 6 hr aerial and root tissues wereseparated and flash frozen in liquid nitrogen prior to storage at −80°C.

Seeds of maize hybrid 35A (Pioneer) were sown in water-moistened sand inflats (10 rows, 5-6 seed/row) and covered with clear, plastic lidsbefore being placed in a growth chamber having 16 hr light (25° C.)/8 hrdark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Coveredflats were watered every three days for 7 days. Seedlings were carefullyremoved from the sand and placed in 1-liter beakers with 150 mM NaCl fortreatment. Control plants were treated with water. After 1 hr, 6 hr, and24 hr aerial and root tissues were separated and flash frozen in liquidnitrogen prior to storage at −80° C.

(1) Heat Shock Treatment

Seeds of Arabidopsis Thaliana (Wassilewskija) were sown in trays andleft at 4° C. for three days to vernalize before being transferred to agrowth chamber with 16 hr light/8 hr dark, 12,000-14,000 Lux, 70%humidity and 20° C., fourteen day old plants were transferred to a 42°C. growth chamber and aerial tissues were harvested 1 hr and 6 hr aftertransfer. Control plants were left at 20° C. and aerial tissues wereharvested. Tissues were flash-frozen in liquid nitrogen and stored at−80° C.

Seeds of maize hybrid 35A (Pioneer) were sown in water-moistened sand inflats (10 rows, 5-6 seed/row) and covered with clear, plastic lidsbefore being placed in a growth chamber having 16 hr light (25° C.)/8 hrdark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Coveredflats were watered every three days for 7 days. Seedlings were carefullyremoved from the sand and placed in 1-liter beakers containing 42° C.water for treatment. Control plants were treated with water at 25° C.After 1 hr and 6 hr aerial and root tissues were separated and flashfrozen in liquid nitrogen prior to storage at −80° C.

(m) Cold Shock Treatment

Seeds of Arabidopsis thaliana (Wassilewskija) were sown in trays andleft at 4° C. for three days to vernalize before being transferred to agrowth chamber having 16 hr light/8 hr dark, 12,000-14,000 LUX, 20° C.and 70% humidity. Fourteen day old plants were transferred to a 4° C.dark growth chamber and aerial tissues were harvested 1 hour and 6 hourslater. Control plants were maintained at 20° C. and covered with foil toavoid exposure to light. Tissues were flash-frozen in liquid nitrogenand stored at −80° C.

Seeds of maize hybrid 35A (Pioneer) were sown in water-moistened sand inflats (10 rows, 5-6 seed/row) and covered with clear, plastic lidsbefore being placed in a growth chamber having 16 hr light (25° C.)/8 hrdark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Coveredflats were watered every three days for 7 days. Seedlings were carefullyremoved from the sand and placed in 1-liter beakers containing 4° C.water for treatment. Control plants were treated with water at 25° C.After 1 hr and 6 hr aerial and root tissues were separated and flashfrozen in liquid nitrogen prior to storage at −80° C.

(n) Arabidopsis Seeds

Fruits (Pod+Seed) 0-5 mm

Seeds of Arabidopsis thaliana (ecotype Wassilewskija) were sown in potsand left at 4° C. for two to three days to vernalize. They were thentransferred to a growth chamber. Plants were grown under long-day (16 hrlight: 8 hr dark) conditions, 7000-8000 LUX light intensity, 70%humidity, and 22° C. temperature. 3-4 siliques (fruits) bearingdeveloping seeds were selected from at least 3 plants and werehand-dissected to determine what developmental stage(s) were representedby the enclosed embryos. Description of the stages of Arabidopsisembryogenesis used in this determination were summarized by Bowman(1994). Silique lengths were then determined and used as an approximatedeterminant for embryonic stage. Siliques 0-5 mm in length containingpost fertilization through pre-heart stage [0-72 hours afterfertilization (HAF)] embryos were harvested and flash frozen in liquidnitrogen.

Fruits (Pod+Seed) 5-10 mm

Seeds of Arabidopsis thaliana (ecotype Wassilewskija) were sown in potsand left at 4° C. for two to three days to vernalize. They were thentransferred to a growth chamber. Plants were grown under long-day (16 hrlight: 8 hr dark) conditions, 7000-8000 LUX light intensity, 70%humidity, and 22° C. temperature. 3-4 siliques (fruits) bearingdeveloping seeds were selected from at least 3 plants and werehand-dissected to determine what developmental stage(s) were representedby the enclosed embryos. Description of the stages of Arabidopsisembryogenesis used in this determination were summarized by Bowman(1994). Silique lengths were then determined and used as an approximatedeterminant for embryonic stage. Siliques 5-10 mm in length containingheart—through early upturned-U-stage [72-120 hours after fertilization(HAF)] embryos were harvested and flash frozen in liquid nitrogen.

Fruits (Pod+Seed)>10 mm

Seeds of Arabidopsis thaliana (ecotype Wassilewskija) were sown in potsand left at 4° C. for two to three days to vernalize. They were thentransferred to a growth chamber. Plants were grown under long-day (16 hrlight: 8 hr dark) conditions, 7000-8000 LUX light intensity, 70%humidity, and 22° C. temperature. 3-4 siliques (fruits) bearingdeveloping seeds were selected from at least 3 plants and werehand-dissected to determine what developmental stage(s) were representedby the enclosed embryos. Description of the stages of Arabidopsisembryogenesis used in this determination were summarized by Bowman(1994). Silique lengths were then determined and used as an approximatedeterminant for embryonic stage. Siliques >10 mm in length containinggreen, late upturned-U-stage [>120 hours after fertilization (HAF)-9days after flowering (DAF)] embryos were harvested and flash frozen inliquid nitrogen.

Green Pods 5-10 mm (Control Tissue for Samples 72-74)

Seeds of Arabidopsis thaliana (ecotype Wassilewskija) were sown in potsand left at 4° C. for two to three days to vernalize. They were thentransferred to a growth chamber. Plants were grown under long-day (16 hrlight: 8 hr dark) conditions, 7000-8000 LUX light intensity, 70%humidity, and 22° C. temperature. 3-4 siliques (fruits) bearingdeveloping seeds were selected from at least 3 plants and werehand-dissected to determine what developmental stage(s) were representedby the enclosed embryos. Description of the stages of Arabidopsisembryogenesis used in this determination were summarized by Bowman(1994). Silique lengths were then determined and used as an approximatedeterminant for embryonic stage. Green siliques 5-10 mm in lengthcontaining developing seeds 72-120 hours after fertilization (HAF)] wereopened and the seeds removed. The remaining tissues (green pods minusseed) were harvested and flash frozen in liquid nitrogen.

Green Seeds from Fruits >10 mm

Seeds of Arabidopsis thaliana (ecotype Wassilewskija) were sown in potsand left at 4° C. for two to three days to vernalize. They were thentransferred to a growth chamber. Plants were grown under long-day (16 hrlight: 8 hr dark) conditions, 7000-8000 LUX light intensity, 70%humidity, and 22° C. temperature. 3-4 siliques (fruits) bearingdeveloping seeds were selected from at least 3 plants and werehand-dissected to determine what developmental stage(s) were representedby the enclosed embryos. Description of the stages of Arabidopsisembryogenesis used in this determination were summarized by Bowman(1994). Silique lengths were then determined and used as an approximatedeterminant for embryonic stage. Green siliques >10 mm in lengthcontaining developing seeds up to 9 days after flowering (DAF)] wereopened and the seeds removed and harvested and flash frozen in liquidnitrogen.

Brown Seeds from Fruits >10 mm

Seeds of Arabidopsis thaliana (ecotype Wassilewskija) were sown in potsand left at 4° C. for two to three days to vernalize. They were thentransferred to a growth chamber. Plants were grown under long-day (16 hrlight: 8 hr dark) conditions, 7000-8000 LUX light intensity, 70%humidity, and 22° C. temperature. 3-4 siliques (fruits) bearingdeveloping seeds were selected from at least 3 plants and werehand-dissected to determine what developmental stage(s) were representedby the enclosed embryos. Description of the stages of Arabidopsisembryogenesis used in this determination were summarized by Bowman(1994). Silique lengths were then determined and used as an approximatedeterminant for embryonic stage. Yellowing siliques >10 mm in lengthcontaining brown, desiccating seeds >11 days after flowering (DAF)] wereopened and the seeds removed and harvested and flash frozen in liquidnitrogen.

Green/Brown Seeds from Fruits >10 mm

Seeds of Arabidopsis thaliana (ecotype Wassilewskija) were sown in potsand left at 4° C. for two to three days to vernalize. They were thentransferred to a growth chamber. Plants were grown under long-day (16 hrlight: 8 hr dark) conditions, 7000-8000 LUX light intensity, 70%humidity, and 22° C. temperature. 3-4 siliques (fruits) bearingdeveloping seeds were selected from at least 3 plants and werehand-dissected to determine what developmental stage(s) were representedby the enclosed embryos. Description of the stages of Arabidopsisembryogenesis used in this determination were summarized by Bowman(1994). Silique lengths were then determined and used as an approximatedeterminant for embryonic stage. Green siliques >10 mm in lengthcontaining both green and brown seeds >9 days after flowering (DAF)]were opened and the seeds removed and harvested and flash frozen inliquid nitrogen.

Mature Seeds (24 Hours after Imbibition)

Mature dry seeds of Arabidopsis thaliana (ecotype Wassilewskija) weresown onto moistened filter paper and left at 4° C. for two to three daysto vernalize. Imbibed seeds were then transferred to a growth chamber[16 hr light: 8 hr dark conditions, 7000-8000 LUX light intensity, 70%humidity, and 22° C. temperature], the emerging seedlings harvestedafter 48 hours and flash frozen in liquid nitrogen.

Mature Seeds (Dry)

Seeds of Arabidopsis thaliana (ecotype Wassilewskija) were sown in potsand left at 4° C. for two to three days to vernalize. They were thentransferred to a growth chamber. Plants were grown under long-day (16 hrlight: 8 hr dark) conditions, 7000-8000 LUX light intensity, 70%humidity, and 22° C. temperature and taken to maturity. Mature dry seedsare collected, dried for one week at 28° C., and vernalized for one weekat 4° C. before used as a source of RNA.

(o) Herbicide Treatment

Arabidopsis thaliana (Ws) seeds were sterilized for 5 min. with 30%bleach, 50 μl Triton in a total volume of 50 ml. Seeds were vernalizedat 4° C. for 3 days before being plated onto GM agar plates at a densityof about 144 seeds per plate. Plates were incubated in a Percival growthchamber having 16 hr light/8 hr dark, 80% relative humidity, 22° C. and11,000 LUX for 14 days.

Plates were sprayed (˜0.5 mls/plate) with water, Finale (1.128 g/L),Glean (1.88 g/L), RoundUp (0.01 g/L) or Trimec (0.08 g/L). Tissue wascollected and flash frozen in liquid nitrogen at the following timepoints: 0, 1, 2, 4, 8, 12 and 24 hours. Frozen tissue was stored at −80°C. prior to RNA isolation.

(p) Root Tips

Seeds of Arabidopsis thaliana (ecotype Ws) were placed on MS plates andvernalized at 4° C. for 3 days before being placed in a 25° C. growthchamber having 16 hr light/8 hr dark, 70% relative humidity and about 3W/m². After 6 days, young seedlings were transferred to flaskscontaining B5 liquid medium, 1% sucrose and 0.05 mg/l indole-3-butyricacid. Flasks were incubated at room temperature with 100 rpm agitation.Media was replaced weekly. After three weeks, roots were harvested andincubated for 1 hr with 2% pectinase, 0.2% cellulase, pH 7 beforestraining through a #80 (Sigma) sieve. The root body material remainingon the sieve (used as the control) was flash frozen and stored at −80°C. until use. The material that passed through the #80 sieve wasstrained through a #200 (Sigma) sieve and the material remaining on thesieve (root tips) was flash frozen and stored at −80° C. until use.Approximately 10 mg of root tips were collected from one flask of rootculture.

Seeds of maize hybrid 35A (Pioneer) were sown in water-moistened sand inflats (10 rows, 5-6 seed/row) and covered with clear, plastic lidsbefore being placed in a growth chamber having 16 hr light (25° C.)/8 hrdark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Coveredflats were watered every three days for 8 days. Seedlings were carefullyremoved from the sand and the root tips (˜2 mm long) were removed andflash frozen in liquid nitrogen prior to storage at −80° C. The tissuesabove the root tips (˜1 cm long) were cut, treated as above and used ascontrol tissue.

(q) Imbibed Seed

Seeds of maize hybrid 35A (Pioneer) were sown in water-moistened sand incovered flats (10 rows, 5-6 seed/row) and covered with clear, plasticlids before being placed in a growth chamber having 16 hr light (25°C.)/8 hr dark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Oneday after sowing, whole seeds were flash frozen in liquid nitrogen priorto storage at −80° C. Two days after sowing, embryos and endosperm wereisolated and flash frozen in liquid nitrogen prior to storage at −80° C.On days 3-6, aerial tissues, roots and endosperm were isolated and flashfrozen in liquid nitrogen prior to storage at −80° C.

(r) Flowers (Green, White or Buds)

Approximately 10 μl of Arabidopsis thaliana seeds (ecotype Ws) were sownon 350 soil (containing 0.03% marathon) and vernalized at 4 C for 3days. Plants were then grown at room temperature under fluorescentlighting until flowering. Flowers were harvested after 28 days in threedifferent categories. Buds that had not opened at all and werecompletely green were categorized as “flower buds” (also referred to asgreen buds by the investigator). Buds that had started to open, withwhite petals emerging slightly were categorized as “green flowers” (alsoreferred to as white buds by the investigator). Flowers that had openedmostly (with no silique elongation) with white petals completely visiblewere categorized as “white flowers” (also referred to as open flowers bythe investigator). Buds and flowers were harvested with forceps, flashfrozen in liquid nitrogen and stored at −80 C until RNA was isolated.

s) Ovules

Seeds of Arabidopsis thaliana heterozygous for pistillata (pi) [ecotypeLandsberg erecta (Ler)] were sown in pots and left at 4° C. for two tothree days to vernalize. They were then transferred to a growth chamber.Plants were grown under long-day (16 hr light: 8 hr dark) conditions,7000-8000 LUX light intensity, 76% humidity, and 24° C. temperature.Inflorescences were harvested from seedlings about 40 days old. Theinflorescences were cut into small pieces and incubated in the followingenzyme solution (pH 5) at room temperature for 0.5-1 hr.: 0.2%pectolyase Y-23, 0.04% pectinase, 5 mM MES, 3% Sucrose and MS salts(1900 mg/l KNO₃, 1650 mg/l NH₄NO₃, 370 mg/l MgSO₄.7H₂O, 170 mg/l KH₂PO₄,440 mg/l CaCl₂.2H₂O, 6.2 mg/l H₂BO₃, 15.6 mg/l MnSO₄.4H₂O, 8.6 mg/lZnSO₄.7H₂O, 0.25 mg/l NaMoO₄.2H₂O, 0.025 mg/l CuCO₄.5H₂O, 0.025 mg/lCoCl₂.6H₂O, 0.83 mg/l KI, 27.8 mg/l FeSO₄.7H₂O, 37.3 mg/l Disodium EDTA,pH 5.8). At the end of the incubation the mixture of inflorescencematerial and enzyme solution was passed through a size 60 sieve and thenthrough a sieve with a pore size of 125 μm. Ovules greater than 125 μmin diameter were collected, rinsed twice in B5 liquid medium (2500 mg/lKNO₃, 250 mg/l MgSO₄.7H₂O, 150 mg/l NaH2PO4.H₂O, 150 mg/l CaCl₂.2H₂O,134 mg/l (NH4)2 CaCl₂.SO₄, 3 mg/l H₂BO₃, 10 mg/l MnSO₄.4H₂O, 2ZnSO₄.7H₂O, 0.25 mg/l NaMoO₄.2H₂O, 0.025 mg/l CuCO₄.5H₂O, 0.025 mg/lCoCl₂.6H₂O, 0.75 mg/l KI, 40 mg/l EDTA sodium ferric salt, 20 g/lsucrose, 10 mg/l Thiamine hydrochloride, 1 mg/l Pyridoxinehydrochloride, 1 mg/l Nicotinic acid, 100 mg/l myo-inositol, pH 5.5)),rinsed once in deionized water and flash frozen in liquid nitrogen. Thesupernatant from the 125 μm sieving was passed through subsequent sievesof 50 μm and 32 μm. The tissue retained in the 32 μm sieve was collectedand mRNA prepared for use as a control.

t) Wounding

Seeds of Arabidopsis thaliana (Wassilewskija) were sown in trays andleft at 4° C. for three days to vernalize before being transferred to agrowth chamber having 16 hr light/8 hr dark, 12,000-14,000 LUX, 70%humidity and 20° C. After 14 days, the leaves were wounded with forceps.Aerial tissues were harvested 1 hour and 6 hours after wounding. Aerialtissues from unwounded plants served as controls. Tissues wereflash-frozen in liquid nitrogen and stored at −80° C.

Seeds of maize hybrid 35A (Pioneer) were sown in water-moistened sand inflats (10 rows, 5-6 seed/row) and covered with clear, plastic lidsbefore being placed in a growth chamber having 16 hr light (25° C.)/8 hrdark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Coveredflats were watered every three days for 7 days. Seedlings were wounded(one leaf nicked by scissors) and placed in 1-liter beakers of water fortreatment. Control plants were treated not wounded. After 1 hr and 6 hraerial and root tissues were separated and flash frozen in liquidnitrogen prior to storage at −80° C.

u) Nitric Oxide Treatment

Seeds of Arabidopsis thaliana (Wassilewskija) were sown in trays andleft at 4° C. for three days to vernalize before being transferred to agrowth chamber having 16 hr light/8 hr dark, 12,000-14,000 LUX, 20° C.and 70% humidity. Fourteen day old plants were sprayed with 5 mM sodiumnitroprusside in a 0.02% Silwett L-77 solution. Control plants weresprayed with a 0.02% Silwett L-77 solution. Aerial tissues wereharvested 1 hour and 6 hours after spraying, flash-frozen in liquidnitrogen and stored at −80° C.

Seeds of maize hybrid 35A (Pioneer) were sown in water-moistened sand inflats (10 rows, 5-6 seed/row) and covered with clear, plastic lidsbefore being placed in a growth chamber having 16 hr light (25° C.)/8 hrdark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Coveredflats were watered every three days for 7 days. Seedlings were carefullyremoved from the sand and placed in 1-liter beakers with 5 mMnitroprusside for treatment. Control plants were treated with water.After 1 hr, 6 hr and 12 hr, aerial and root tissues were separated andflash frozen in liquid nitrogen prior to storage at −80° C.

v) Root Hairless mutants

Plants mutant at the rhl gene locus lack root hairs. This mutation ismaintained as a heterozygote.

Seeds of Arabidopsis thaliana (Landsberg erecta) mutated at the rhl genelocus were sterilized using 30% bleach with 1 ul/ml 20% Triton-X 100 andthen vernalized at 4° C. for 3 days before being plated onto GM agarplates. Plates were placed in growth chamber with 16 hr light/8 hr.dark, 23° C., 14,500-15,900 LUX, and 70% relative humidity forgermination and growth.

After 7 days, seedlings were inspected for root hairs using a dissectingmicroscope. Mutants were harvested and the cotyledons removed so thatonly root tissue remained. Tissue was then flash frozen in liquidnitrogen and stored at −80 C.

Arabidopsis thaliana (Landsberg erecta) seedlings grown and prepared asabove were used as controls.

Alternatively, seeds of Arabidopsis thaliana (Landsberg erecta),heterozygous for the rhl1 (root hairless) mutation, weresurface-sterilized in 30% bleach containing 0.1% Triton X-100 andfurther rinsed in sterile water. They were then vernalized at 4° C. for4 days before being plated onto MS agar plates. The plates weremaintained in a growth chamber at 24° C. with 16 hr light/8 hr dark forgermination and growth. After 10 days, seedling roots that expressed thephenotype (i.e. lacking root hairs) were cut below the hypocotyljunction, frozen in liquid nitrogen and stored at −80° C. Thoseseedlings with the normal root phenotype (heterozygous or wt) werecollected as described for the mutant and used as controls.

w) Ap2

Seeds of Arabidopsis thaliana (ecotype Landesberg erecta) and floralmutant apetala2 (Jofuku et al., 1994, Plant Cell 6:1211-1225) were sownin pots and left at 4° C. for two to three days to vernalize. They werethen transferred to a growth chamber. Plants were grown under long-day(16 hr light, 8 hr dark) conditions 7000-8000 LUX light intensity, 70%humidity and 22° C. temperature. Inflorescences containing immaturefloral buds (stages 1-7; Bowman, 1994) as well as the inflorescencemeristem were harvested and flashfrozen. Polysomal polyA+ RNA wasisolated from tissue according to Cox and Goldberg, 1988).

x) Salt

Arabidopsis thaliana ecotype Ws seeds were vernalized at 4° C. for 3days before sowing in flats containing vermiculite soil. Flats wereplaced at 20° C. in a Conviron growth chamber having 16 hr light/8 hrdark. Whole plants (used as controls) received water. Other plants weretreated with 100 mM NaCl. After 6 hr and 72 hr, aerial and root tissueswere harvested and flash frozen in liquid nitrogen prior to storage at−80° C.

y) Petals

Arabidopsis thaliana ecotype Ws seeds were vernalized at 4° C. for 3days before sowing in flats containing vermiculite soil. Flats werewatered placed at 20° C. in a Conviron growth chamber having 16 hrlight/8 hr dark. Whole plants (used as the control) and petals frominflorescences 23-25 days after germination were harvested, flash frozenin liquid nitrogen and stored at −80° C.

z) Pollen

Arabidopsis thaliana ecotype Ws seeds were vernalized at 4° C. for 3days before sowing in flats containing vermiculite soil. Flats werewatered and placed at 20° C. in a Conviron growth chamber having 16 hrlight/8 hr dark. Whole plants (used as controls) and pollen from plants38 dap was harvested, flash frozen in liquid nitrogen and stored at −80°C.

aa) Interploidy Crosses

Interploidy crosses involving a 6× parent are lethal. Crosses involvinga 4× parent are complete and analyzed. The imbalance in thematernal/paternal ratio produced from the cross can lead to big seeds.Arabidopsis thaliana ecotype Ws seeds were vernalized at 4° C. for 3days before sowing. Small siliques were harvested at 5 days afterpollination, flash frozen in liquid nitrogen and stored at −80° C.

bb) Line Comparisons

Alkaloid 35S over-expressing lines were used to monitor the expressionlevels of terpenoid/alkaloid biosynthetic and P450 genes to identify thetranscriptional regulatory points I the biosynthesis pathway and therelated P450 genes. Arabidopsis thaliana ecotype Ws seeds werevernalized at 4° C. for 3 days before sowing in vermiculite soil(Zonolite) supplemented by Hoagland solution. Flats were placed inConviron growth chambers under long day conditions (16 hr light, 23°C./8 hr dark, 20° C.) Basta spray and selection of the overexpressinglines was conducted about 2 weeks after germination. Approximately 2-3weeks after bolting (approximately 5-6 weeks after germination), stemand siliques from the over-expressing lines and from wild-type plantswere harvested, flash frozen in liquid nitrogen and stored at −80° C.

cc) DMT-II

Demeter (dmt) is a mutant of a methyl transferase gene and is similar tofie. Arabidopsis thaliana ecotype Ws seeds were vernalized at 4° C. for3 days before sowing. Cauline leaves and closed flowers were isolatedfrom 35S::DMT and dmt −/− plant lines, flash frozen in liquid nitrogenand stored at −80° C.

dd) CS6630 Roots and Shoots

Arabidopsis thaliana ecotype Ws seeds were vernalized at 4° C. for 3days before sowing on MS media (1%) sucrose on bactor-agar. Roots andshoots were separated 14 days after germination, flash frozen in liquidnitrogen and stored at −80° C.

ee) CS237

CS237 is an ethylene triple response mutant that is insensitive toethylene and which has an etr1-1 phenotype. Arabidopsis thaliana CS237seeds were vernalized at 4° C. for 3 days before sowing. Aerial tissuewas collected from mutants and wild-type Columbia ecotype plants, flashfrozen in liquid nitrogen and stored at −80° C.

ff) Guard Cells

Arabidopsis thaliana ecotype Ws seeds were vernalized at 4° C. for 3days before sowing. Leaves were harvested, homogenized and centrifugedto isolate the guard cell containing fraction. Homogenate from leavesserved as the control. Samples were flash frozen in liquid nitrogen andstored at −80° C. Identical experiments using leaf tissue from canolawere performed.

gg) 3642-1

3642-1 is a T-DNA mutant that affects leaf development. This mutantsegregates 3:1, wild-type:mutant. Arabidopsis thaliana 3642-1 mutantseeds were vernalized at 4° C. for 3 days before sowing in flats ofMetroMix 200. Flats were placed in the greenhouse, watered and grown tothe 8 leaf, pre-flower stage. Stems and rosette leaves were harvestedfrom the mutants and the wild-type segregants, flash frozen and storedat −80° C.

hh) Caf

Carp1e factory (Caf) is a double-stranded RNAse protein that ishypothesized to process small RNAs in Arabidopsis. The protein isclosely related to a Drosophila protein named DICER that functions inthe RNA degradation steps of RNA interference. Arabidopsis thaliana Cafmutant seeds were vernalized at 4° C. for 3 days before sowing in flatsof MetroMix 200. Flats were placed in the greenhouse, watered and grownto the 8 leaf, pre-flower stage. Stems and rosette leaves were harvestedfrom the mutants and the wild-type segregants, flash frozen and storedat −80° C.

2. Microarray Hybridization Procedures

Microarray technology provides the ability to monitor mRNA transcriptlevels of thousands of genes in a single experiment. These experimentssimultaneously hybridize two differentially labeled fluorescent cDNApools to glass slides that have been previously spotted with cDNA clonesof the same species. Each arrayed cDNA spot will have a correspondingratio of fluorescence that represents the level of disparity between therespective mRNA species in the two sample pools. Thousands ofpolynucleotides can be spotted on one slide, and each experimentgenerates a global expression pattern.

Coating Slides

The microarray consists of a chemically coated microscope slide,referred herein as a “chip” with numerous polynucleotide samples arrayedat a high density. The poly-L-lysine coating allows for this spotting athigh density by providing a hydrophobic surface, reducing the spreadingof spots of DNA solution arrayed on the slides. Glass microscope slides(Gold Seal #3010 manufactured by Gold Seal Products, Portsmouth, N.H.,USA) were coated with a 0.1% W/V solution of Poly-L-lysine (Sigma, St.Louis, Mo.) using the following protocol:

-   1. Slides were placed in slide racks (Shandon Lipshaw #121). The    racks were then put in chambers (Shandon Lipshaw #121).-   2. Cleaning solution was prepared:    -   70 g NaOH was dissolved in 280 mL ddH₂O.    -   420 mL 95% ethanol was added. The total volume was 700 mL        (=2×350 mL); it was stirred until completely mixed. If the        solution remained cloudy, ddH₂O was added until clear.-   3. The solution was poured into chambers with slides; the chambers    were covered with glass lids. The solution was mixed on an orbital    shaker for 2 hr.-   4. The racks were quickly transferred to fresh chambers filled with    ddH₂O. They were rinsed vigorously by plunging racks up and down.    Rinses were repeated 4× with fresh ddH₂O each time, to remove all    traces of NaOH-ethanol.-   5. Polylysine solution was prepared:    -   0 mL poly-L-lysine+70 mL tissue culture PBS in 560 mL water,        using plastic graduated cylinder and beaker.-   6. Slides were transferred to polylysine solution and shaken for 1    hr.-   7. The rack was transferred to a fresh chambers filled with ddH₂O.    It was plunged up and down 5× to rinse.-   8. The slides were centrifuged on microtiter plate carriers (paper    towels were placed below the rack to absorb liquid) for 5 min. @ 500    rpm. The slide racks were transferred to empty chambers with covers.-   9. Slide racks were dried in a 45 C oven for 10 min.-   10. The slides were stored in a closed plastic slide box.-   11. Normally, the surface of lysine coated slides was not very    hydrophobic immediately after this process, but became increasingly    hydrophobic with storage. A hydrophobic surface helped ensure that    spots didn't run together while printing at high densities. After    they aged for 10 days to a month the slides were ready to use.    However, coated slides that have been sitting around for long    periods of time were usually too old to be used. This was because    they developed opaque patches, visible when held to the light, and    these resulted in high background hybridization from the fluorescent    probe. Alternatively, pre-coated glass slides were purchased from    TeleChem International, Inc. (Sunnyvale, Calif., 94089; catalog    number SMM-25, Superamine substrates).    PCR Amplification of cDNA Clone Inserts

Polynucleotides were amplified from Arabidopsis cDNA clones using insertspecific probes. The resulting 100 uL PCR reactions were purified withQiaquick 96 PCR purification columns (Qiagen, Valencia, Calif., USA) andeluted in 30 uL of 5 mM Tris. 8.5 uL of the elution were mixed with 1.5uL of 20×SSC to give a final spotting solution of DNA in 3×SSC. Theconcentrations of DNA generated from each clone varied between 10-100ng/ul, but were usually about 50 ng/ul.

Arraying of PCR Products on Glass Slides

PCR products from cDNA clones were spotted onto the poly-L-Lysine coatedglass slides using an arrangement of quill-tip pins (ChipMaker 3spotting pins; Telechem, International, Inc., Sunnyvale, Calif., USA)and a robotic arrayer (PixSys 3500, Cartesian Technologies, Irvine,Calif., USA). Around 0.5 nl of a prepared PCR product was spotted ateach location to produce spots with approximately 100 um diameters. Spotcenter-to-center spacing was from 180 um to 210 um depending on thearray. Printing was conducted in a chamber with relative humidity set at50%.

Slides containing maize sequences were purchased from Agilent Technology(Palo Alto, Calif. 94304).

Post-Processing of Slides

After arraying, slides were processed through a series ofsteps—rehydration, UV cross-linking, blocking and denaturation—requiredprior to hybridization. Slides were rehydrated by placing them over abeaker of warm water (DNA face down), for 2-3 sec, to distribute the DNAmore evenly within the spots, and then snap dried on a hot plate (DNAside, face up). The DNA was then cross-linked to the slides by UVirradiation (60-65 mJ; 2400 Stratalinker, Stratagene, La Jolla, Calif.,USA).

Following this a blocking step was performed to modify remaining freelysine groups, and hence minimize their ability to bind labeled probeDNA. To achieve this the arrays were placed in a slide rack. An emptyslide chamber was left ready on an orbital shaker. The rack was bentslightly inwards in the middle, to ensure the slides would not run intoeach other while shaking. The blocking solution was prepared as follows:

3×350-ml glass chambers (with metal tops) were set to one side, and alarge round Pyrex dish with dH₂O was placed ready in the microwave. Atthis time, 15 ml sodium borate was prepared in a 50 ml conical tube.

6-g succinic anhydride was dissolved in approx. 325-350 mL1-methyl-2-pyrrolidinone. Rapid addition of reagent was crucial.

a. Immediately after the last flake of the succinic anhydride dissolved,the 15-mL sodium borate was added.

b. Immediately after the sodium borate solution mixed in, the solutionwas poured into an empty slide chamber.

c. The slide rack was plunged rapidly and evenly in the solution. It wasvigorously shaken up and down for a few seconds, making sure slidesnever left the solution.

d. It was mixed on an orbital shaker for 15-20 min. Meanwhile, the waterin the Pyrex dish (enough to cover slide rack) was heated to boiling.

Following this, the slide rack was gently plunge in the 95 C water (juststopped boiling) for 2 min. Then the slide rack was plunged 5× in 95%ethanol. The slides and rack were centrifuged for 5 min. @ 500 rpm. Theslides were loaded quickly and evenly onto the carriers to avoidstreaking. The arrays were used immediately or store in slide box.

The Hybridization process began with the isolation of mRNA from the twotissues (see “Isolation of total RNA” and “Isolation of mRNA”, below) inquestion followed by their conversion to single stranded cDNA (see“Generation of probes for hybridization”, below). The cDNA from eachtissue was independently labeled with a different fluorescent dye andthen both samples were pooled together. This final differentiallylabeled cDNA pool was then placed on a processed microarray and allowedto hybridize (see “Hybridization and wash conditions”, below).

Isolation of Total RNA

Approximately 1 g of plant tissue was ground in liquid nitrogen to afine powder and transferred into a 50-ml centrifuge tube containing 10ml of Trizol reagent. The tube was vigorously vortexed for 1 min andthen incubated at room temperature for 10-20 min. on an orbital shakerat 220 rpm. Two ml of chloroform was added to the tube and the solutionvortexed vigorously for at least 30-sec before again incubating at roomtemperature with shaking. The sample was then centrifuged at 12,000×g(10,000 rpm) for 15-20 min at 4° C. The aqueous layer was removed andmixed by inversion with 2.5 ml of 1.2 M NaCl/0.8 M Sodium Citrate and2.5 ml of isopropyl alcohol added. After a 10 min. incubation at roomtemperature, the sample was centrifuged at 12,000×g (10,000 rpm) for 15min at 4° C. The pellet was washed with 70% ethanol, re-centrifuged at8,000 rpm for 5 min and then air dried at room temperature for 10 min.The resulting total RNA was dissolved in either TE (10 mM Tris-HCl, 1 mMEDTA, pH 8.0) or DEPC (diethylpyrocarbonate) treated deionized water(RNAse-free water). For subsequent isolation of mRNA using the Qiagenkit, the total RNA pellet was dissolved in RNAse-free water.

Isolation of mRNA

mRNA was isolated using the Qiagen Oligotex mRNA Spin-Column protocol(Qiagen, Valencia, Calif.). Briefly, 500 μl OBB buffer (20 mM Tris-Cl,pH 7.5, 1 M NaCl, 2 mM EDTA, 0.2% SDS) was added to 500 μl of total RNA(0.5-0.75 mg) and mixed thoroughly. The sample was first incubated at70° C. for 3 min, then at room temperature for 10 minutes and finallycentrifuged for 2 min at 14,000-18,000×g. The pellet was resuspended in400 μl OW2 buffer (10 mM Tris-Cl, pH 7.5, 150 mM NaCl, 1 mM EDTA) byvortexing, the resulting solution placed on a small spin column in a 1.5ml RNase-free microcentrifuge tube and centrifuged for 1 min at14,000-18,000×g. The spin column was transferred to a new 1.5 mlRNase-free microcentrifuge tube and washed with 400 μl of OW2 buffer. Torelease the isolated mRNA from the resin, the spin column was againtransferred to a new RNase-free 1.5 ml microcentrifuge tube, 20-100 μl70° C. OEB buffer (5 mM Tris-Cl, pH 7.5) added and the resin resuspendedin the resulting solution via pipetting. The mRNA solution was collectedafter centrifuging for 1 min at 14,000-18,000×g.

Alternatively, mRNA was isolated using the Stratagene Poly(A) Quik mRNAIsolation Kit (Startagene, La Jolla, Calif.). Here, up to 0.5 mg oftotal RNA (maximum volume of 1 ml) was incubated at 65° C. for 5minutes, snap cooled on ice and 0.1× volumes of 10× sample buffer (10 mMTris-HCl (pH 7.5), 1 mM EDTA (pH 8.0) 5 M NaCl) added. The RNA samplewas applied to a prepared push column and passed through the column at arate of ˜1 drop every 2 sec. The solution collected was reapplied to thecolumn and collected as above. 200 μl of high salt buffer (10 mMTris-HCl (pH 7.5), 1 mM EDTA, 0.5 NaCl) was applied to the column andpassed through the column at a rate of ˜1 drop every 2 sec. This stepwas repeated and followed by three low salt buffer (10 mM Tris-HCl (pH7.5), 1 mM EDTA, 0.1 M NaCl) washes preformed in a similar manner. mRNAwas eluted by applying to the column four separate 200 μl aliquots ofelution buffer (10 mM Tris-HCl (pH 7.5), 1 mM EDTA) preheated to 65° C.Here, the elution buffer was passed through the column at a rate of 1drop/sec. The resulting mRNA solution was precipitated by adding 0.1×volumes of 10× sample buffer, 2.5 volumes of ice-cold 100% ethanol,incubating overnight at −20° C. and centrifuging at 14,000-18,000×g for20-30 min at 4° C. The pellet was washed with 70% ethanol and air driedfor 10 min. at room temperature before resuspension in RNase-freedeionized water.

Preparation of Yeast Controls

Plasmid DNA was isolated from the following yeast clones using Qiagenfiltered maxiprep kits (Qiagen, Valencia, Calif.): YAL022c(Fun26),YAL031c(Fun21), YBR032w, YDL131w, YDL182w, YDL194w, YDL196w, YDR050c andYDR116c. Plasmid DNA was linearized with either BsrBI (YAL022c(Fun26),YAL031c(Fun21), YDL131w, YDL182w, YDL194w, YDL196w, YDR050c) or AflIII(YBR032w, YDR116c) and isolated.

In Vitro Transcription of Yeast Clones

The following solution was incubated at 37° C. for 2 hours: 17 μl ofisolated yeast insert DNA (1 μg), 20 μl 5× buffer, 10 μl 100 mM DTT, 2.5μl (100 U) RNasin, 20 μl 2.5 mM (ea.) rNTPs, 2.7 μl (40 U) SP6polymerase and 27.8 μl RNase-free deionized water. 2 μl (2 U) AmpliDNase I was added and the incubation continued for another 15 min. 10 μl5M NH₄OAC and 100 μl phenol:chloroform:isoamyl alcohol (25:24:1) wereadded, the solution vortexed and then centrifuged to separate thephases. To precipitate the RNA, 250 μl ethanol was added and thesolution incubated at −20° C. for at least one hour. The sample was thencentrifuged for 20 min at 4° C. at 14,000-18,000×g, the pellet washedwith 500 μl of 70% ethanol, air dried at room temperature for 10 min andresuspended in 100 μl of RNase-free deionized water. The precipitationprocedure was then repeated.

Alternatively, after the two-hour incubation, the solution was extractedwith phenol/chloroform once before adding 0.1 volume 3M sodium acetateand 2.5 volumes of 100% ethanol. The solution was centrifuged at 15,000rpm, 4° C. for 20 minutes and the pellet resuspended in RNase-freedeionized water. The DNase I treatment was carried out at 37° C. for 30minutes using 2 U of Ampli DNase I in the following reaction condition:50 mM Tris-HCl (pH 7.5), 10 mM MgCl₂. The DNase I reaction was thenstopped with the addition of NH₄OAC and phenol:chloroform:isoamylalcohol (25:24:1), and RNA isolated as described above.

0.15-2.5 ng of the in vitro transcript RNA from each yeast clone wereadded to each plant mRNA sample prior to labeling to serve as positive(internal) probe controls.

Generation of Probes for Hybridization

Generation of Labeled Probes for Hybridization from First-Strand cDNA

Hybridization probes were generated from isolated mRNA using an Atlas™Glass Fluorescent Labeling Kit (Clontech Laboratories, Inc., Palo Alto,Calif., USA). This entails a two step labeling procedure that firstincorporates primary aliphatic amino groups during cDNA synthesis andthen couples fluorescent dye to the cDNA by reaction with the aminofunctional groups. Briefly, 5 μg of oligo(dT)₁₈ primerd(TTTTTTTTTTTTTTTTTTV) was mixed with Poly A+ mRNA (1.5-2 μg mRNAisolated using the Qiagen Oligotex mRNA Spin-Column protocol or-theStratagene Poly(A) Quik mRNA Isolation protocol (Stratagene, La Jolla,Calif., USA)) in a total volume of 25 μl. The sample was incubated in athermocycler at 70° C. for 5 min, cooled to 48° C. and 10 μl of 5× cDNASynthesis Buffer (kit supplied), 5 μl 10× dNTP mix (dATP, dCTP, dGTP,dTTP and aminoallyl-dUTP; kit supplied), 7.5 μl deionized water and 2.5μl MMLV Reverse Transcriptase (500 U) added. The reaction was thenincubated at 48° C. for 30 minutes, followed by 1 hr incubation at 42°C. At the end of the incubation the reaction was heated to 70° C. for 10min, cooled to 37° C. and 0.5 μl (5 U) RNase H added, before incubatingfor 15 min at 37° C. The solution was vortexed for 1 min after theaddition of 0.5 μl 0.5 M EDTA and 5 μl of QuickClean Resin (kitsupplied) then centrifuged at 14,000-18,000×g for 1 min. After removingthe supernatant to a 0.45 μm spin filter (kit supplied), the sample wasagain centrifuged at 14,000-18,000×g for 1 min, and 5.5 μl 3 M sodiumacetate and 137.5 μl of 100% ethanol added to the sample beforeincubating at −20° C. for at least 1 hr. The sample was then centrifugedat 14,000-18,000×g at 4° C. for 20 min, the resulting pellet washed with500 μl 70% ethanol, air-dried at room temperature for 10 min andresuspended in 10 μl of 2× fluorescent labeling buffer (kit provided).10 μl each of the fluorescent dyes Cy3 and Cy5 (Amersham Pharmacia(Piscataway, N.J., USA); prepared according to Atlas™ kit directions ofClontech) were added and the sample incubated in the dark at roomtemperature for 30 min.

The fluorescently labeled first strand cDNA was precipitated by adding 2μl 3M sodium acetate and 50 μl 100% ethanol, incubated at −20° C. for atleast 2 hrs, centrifuged at 14,000-18,000×g for 20 min, washed with 70%ethanol, air-dried for 10 min and dissolved in 100 μl of water.

Alternatively, 3-4 μg mRNA, 2.5 (˜8.9 ng of in vitro translated mRNA) μlyeast control and 3 μg oligo dTV (TTTTTTTTTTTTTTTTTT(A/C/G) were mixedin a total volume of 24.7 μl. The sample was incubated in a thermocyclerat 70° C. for 10 min. before chilling on ice. To this, 8 μl of 5× firststrand buffer (SuperScript II RNase H—Reverse Transcriptase kit fromInvitrogen (Carlsbad, Calif. 92008); cat no. 18064022), 0.8° C. ofaa-dUTP/dNTP mix (50×; 25 mM dATP, 25 mM dGTP, 25 mM dCTP, 15 mM dTTP,10 mM aminoallyl-dUTP), 4 μl of 0.1 M DTT and 2.5 μl (500 units) ofSuperscript R.T.II enzyme (Stratagene) were added. The sample wasincubated at 42° C. for 2 hours before a mixture of 10° C. of 1M NaOHand 10° C. of 0.5 M EDTA were added. After a 15 minute incubation at 65°C., 25 μl of 1 M Tris pH 7.4 was added. This was mixed with 450 μl ofwater in a Microcon 30 column before centrifugation at 11,000×g for 12min. The column was washed twice with 450 μl (centrifugation at 11,000g, 12 min.) before eluting the sample by inverting the Microcon columnand centrifuging at 11,000×g for 20 seconds. Sample was dehydrated bycentrifugation under vacuum and stored at −20° C.

Each reaction pellet was dissolved in 9 μl of 0.1 M carbonate buffer(0.1M sodium carbonate and sodium bicarbonate, pH=8.5-9) and 4.5 μl ofthis placed in two microfuge tubes. 4.5 μl of each dye (in DMSO) wereadded and the mixture incubated in the dark for 1 hour. 4.5 μl of 4 Mhydroxylamine was added and again incubated in the dark for 15 minutes.

Regardless of the method used for probe generation, the probe waspurified using a Qiagen PCR cleanup kit (Qiagen, Valencia, Calif., USA),and eluted with 100 ul EB (kit provided). The sample was loaded on aMicrocon YM-30 (Millipore, Bedford, Mass., USA) spin column andconcentrated to 4-5 ul in volume. Probes for the maize microarrays weregenerated using the Fluorescent Linear Amplification Kit (cat. No.G2556A) from Agilent Technologies (Palo Alto, Calif.).

Hybridization and Wash Conditions

The following Hybridization and Washing Condition were developed:

Hybridization Conditions:

Labeled probe was heated at 95° C. for 3 min and chilled on ice. Then 25□L of the hybridization buffer which was warmed at 42 C was added to theprobe, mixing by pipetting, to give a final concentration of:

50% formamide

4×SSC

0.03% SDS

5×Denhardt's solution

0.1 μg/ml single-stranded salmon sperm DNA

The probe was kept at 42 C. Prior to the hybridization, the probe washeated for 1 more min., added to the array, and then covered with aglass cover slip. Slides were placed in hybridization chambers(Telechem, Sunnyvale, Calif.) and incubated at 42° C. overnight.

Washing Conditions:

-   A. Slides were washed in 1×SSC+0.03% SDS solution at room    temperature for 5 minutes,-   B. Slides were washed in 0.2×SSC at room temperature for 5 minutes,-   C. Slides were washed in 0.05×SSC at room temperature for 5 minutes.

After A, B, and C, slides were spun at 800×g for 2 min. to dry. Theywere then scanned.

Maize microarrays were hybridized according to the instructions includedFluorescent Linear Amplification Kit (cat. No. G2556A) from AgilentTechnologies (Palo Alto, Calif.).

Scanning of Slides

The chips were scanned using a ScanArray 3000 or 5000 (General Scanning,Watertown, Mass., USA). The chips were scanned at 543 and 633 nm, at 10um resolution to measure the intensity of the two fluorescent dyesincorporated into the samples hybridized to the chips.

Data Extraction and Analysis

The images generated by scanning slides consisted of two 16-bit TIFFimages representing the fluorescent emissions of the two samples at eacharrayed spot. These images were then quantified and processed forexpression analysis using the data extraction software Imagene™(Biodiscovery, Los Angeles, Calif., USA). Imagene output wassubsequently analyzed using the analysis program Genespring™ (SiliconGenetics, San Carlos, Calif., USA). In Genespring, the data was importedusing median pixel intensity measurements derived from Imagene output.Background subtraction, ratio calculation and normalization were allconducted in Genespring. Normalization was achieved by breaking the datain to 32 groups, each of which represented one of the 32 pin printingregions on the microarray. Groups consist of 360 to 550 spots. Eachgroup was independently normalized by setting the median of ratios toone and multiplying ratios by the appropriate factor.

Results

The results of the microarray experiments are set forth in Table 1 inthe section entitled “Microarray Data” which shows the results of thedifferential expression experiments for the mRNAs, as reported by theircorresponding cDNA ID number, that were differentially transcribed undera particular set of conditions as compared to a control sample. The cDNAID numbers correspond to those utilized. Increases in mRNA abundancelevels in experimental plants versus the controls are denoted with theplus sign (+). Likewise, reductions in mRNA abundance levels in theexperimental plants are denoted with the minus (−) sign.

The Table 1 section entitled “Microarray Data” is organized according tothe clone number with each set of experimental conditions being denotedby the term “Expt Rep ID:” followed by a “short name”. The row titled“Microarray Experiment Parameters” links each “short name” with a shortdescription of the experiment and the parameters.

The sequences showing differential expression in a particular experiment(denoted by either a “+” or “−” in the column in Table 1 entitled“SIGNCLOG_RATIO”) thereby show utility for a function in a plant, andthese functions/utilities are described in detail below, where the titleof each section (i.e. a “utility section”) is correlated with theparticular differential expression experiment in the section of Table 1entitled “Microarray Experiment Parameters”.

Organ-Affecting Genes, Gene Components, Products (IncludingDifferentiation and Function)

Root Genes

The economic values of roots arise not only from harvested adventitiousroots or tubers, but also from the ability of roots to funnel nutrientsto support growth of all plants and increase their vegetative material,seeds, fruits, etc. Roots have four main functions. First, they anchorthe plant in the soil. Second, they facilitate and regulate themolecular signals and molecular traffic between the plant, soil, andsoil fauna. Third, the root provides a plant with nutrients gained fromthe soil or growth medium. Fourth, they condition local soil chemicaland physical properties.

Root genes are active or potentially active to a greater extent in rootsthan in most other organs of the plant. These genes and gene productscan regulate many plant traits from yield to stress tolerance. Rootgenes can be used to modulate root growth and development.

Differential Expression of the Sequences in Roots

The relative levels of mRNA product in the root versus the aerialportion of the plant was measured. Specifically, mRNA was isolated fromroots and root tips of Arabidopsis plants and compared to mRNA isolatedfrom the aerial portion of the plants utilizing microarray procedures.

Root Hair Genes, Gene Components and Products

Root hairs are specialized outgrowths of single epidermal cells termedtrichoblasts. In many and perhaps all species of plants, thetrichoblasts are regularly arranged around the perimeter of the root. InArabidopsis, for example, trichoblasts tend to alternate with non-haircells or atrichoblasts. This spatial patterning of the root epidermis isunder genetic control, and a variety of mutants have been isolated inwhich this spacing is altered or in which root hairs are completelyabsent.

The root hair development genes of the instant invention are useful tomodulate one or more processes of root hair structure and/or functionincluding (1) development; (2) interaction with the soil and soilcontents; (3) uptake and transport in the plant; and (4) interactionwith microorganisms.

1.) Development

The surface cells of roots can develop into single epidermal cellstermed trichoblasts or root hairs. Some of the root hairs will persistfor the life of the plant; others will gradually die back; some maycease to function due to external influences. These genes and geneproducts can be used to modulate root hair density or root hair growth;including rate, timing, direction, and size, for example. These genesand gene products can also be used to modulate cell properties such ascell size, cell division, rate and direction and number, cellelongation, cell differentiation, lignified cell walls, epidermal cells(including trichoblasts) and root apical meristem cells (growth andinitiation); and root hair architecture such as leaf cells under thetrichome, cells forming the base of the trichome, trichome cells, androot hair responses. In addition these genes and gene products can beused to modulate one or more of the growth and development processes inresponse to internal plant programs or environmental stimuli in, forexample, the seminal system, nodal system, hormone responses, Auxin,root cap abscission, root senescence, gravitropism, coordination of rootgrowth and development with that of other organs (including leaves,flowers, seeds, fruits, and stems), and changes in soil environment(including water, minerals, Ph, and microfauna and flora).2.) Interaction with Soil and Soil ContentsRoot hairs are sites of intense chemical and biological activity and asa result can strongly modify the soil they contact. Roots hairs can becoated with surfactants and mucilage to facilitate these activities.Specifically, roots hairs are responsible for nutrient uptake bymobilizing and assimilating water, reluctant ions, organic and inorganiccompounds and chemicals. In addition, they attract and interact withbeneficial microfauna and flora. Root hairs also help to mitigate theeffects of toxic ions, pathogens and stress. Thus, root hair genes andgene products can be used to modulate traits such as root hairsurfactant and mucilage (including composition and secretion rate andtime); nutrient uptake (including water, nitrate and other sources ofnitrogen, phosphate, potassium, and micronutrients (e.g. iron, copper,etc.); microbe and nematode associations (such as bacteria includingnitrogen-fixing bacteria, mycorrhizae, nodule-forming and othernematodes, and nitrogen fixation); oxygen transpiration; detoxificationeffects of iron, aluminum, cadium, mercury, salt, and other soilconstituents; pathogens (including chemical repellents) glucosinolates(GSL1), which release pathogen-controlling isothiocyanates; and changesin soil (such as Ph, mineral excess and depletion), and rhizosheath.3.) Transport of Materials in PlantsUptake of the nutrients by the root and root hairs contributes asource-sink effect in a plant. The greater source of nutrients, the moresinks, such as stems, leaves, flowers, seeds, fruits, etc. can drawsustenance to grow. Thus, root hair development genes and gene productscan be used to modulate the vigor and yield of the overall plant as wellas distinct cells, organs, or tissues of a plant. The genes and geneproducts, therefore, can modulate plant nutrition, growth rate (such aswhole plant, including height, flowering time, etc., seedling,coleoptile elongation, young leaves, stems, flowers, seeds and fruit)and yield, including biomass (fresh and dry weight during any time inplant life, including maturation and senescence), number of flowers,number of seeds, seed yield, number, size, weight and harvest index(content and composition, e.g. amino acid, jasmonate, oil, protein andstarch) and fruit yield (number, size, weight, harvest index, and postharvest quality).Reproduction Genes, Gene Components and Products

Reproduction genes are defined as genes or components of genes capableof modulating any aspect of sexual reproduction from flowering time andinflorescence development to fertilization and finally seed and fruitdevelopment. These genes are of great economic interest as well asbiological importance. The fruit and vegeTable industry grosses over $1billion USD a year. The seed market, valued at approximately $15 billionUSD annually, is even more lucrative.

Inflorescence and Floral Development Genes, Gene Components and Products

During reproductive growth the plant enters a program of floraldevelopment that culminates in fertilization, followed by the productionof seeds. Senescence may or may not follow. The flower formation is aprecondition for the sexual propagation of plants and is thereforeessential for the propagation of plants that cannot be propagatedvegetatively as well as for the formation of seeds and fruits. The pointof time at which the merely vegetative growth of plants changes intoflower formation is of vital importance for example in agriculture,horticulture and plant breeding. Also the number of flowers is often ofeconomic importance, for example in the case of various useful plants(tomato, cucumber, zucchini, cotton etc.) with which an increased numberof flowers may lead to an increased yield, or in the case of growingornamental plants and cut flowers.

Flowering plants exhibit one of two types of inflorescence architecture:indeterminate, in which the inflorescence grows indefinitely, ordeterminate, in which a terminal flower is produced. Adult organs offlowering plants develop from groups of stem cells called meristems. Theidentity of a meristem is inferred from structures it produces:vegetative meristems give rise to roots and leaves, inflorescencemeristems give rise to flower meristems, and flower meristems give riseto floral organs such as sepals and petals. Not only are meristemscapable of generating new meristems of different identity, but their ownidentity can change during development. For example, a vegetative shootmeristem can be transformed into an inflorescence meristem upon floralinduction, and in some species, the inflorescence meristem itself willeventually become a flower meristem. Despite the importance of meristemtransitions in plant development, little is known about the underlyingmechanisms.

Following germination, the shoot meristem produces a series of leafmeristems on its flanks. However, once floral induction has occurred,the shoot meristem switches to the production of flower meristems.Flower meristems produce floral organ primordia, which developindividually into sepals, petals, stamens or carpels. Thus, flowerformation can be thought of as a series of distinct developmental steps,i.e. floral induction, the formation of flower primordia and theproduction of flower organs. Mutations disrupting each of the steps havebeen isolated in a variety of species, suggesting that a genetichierarchy directs the flowering process (see for review, Weigel andMeyerowitz, In Molecular Basis of Morphogenesis (ed. M. Bernfield). 51stAnnual Symposium of the Society for Developmental Biology, pp. 93-107,New York, 1993).

Expression of many reproduction genes and gene products is orchestratedby internal programs or the surrounding environment of a plant. Thesegenes can be used to modulate traits such as fruit and seed yield

Seed and Fruit Development Genes, Gene Components and Products

The ovule is the primary female sexual reproductive organ of floweringplants. At maturity it contains the egg cell and one large central cellcontaining two polar nuclei encased by two integuments that, afterfertilization, develops into the embryo, endosperm, and seed coat of themature seed, respectively. As the ovule develops into the seed, theovary matures into the fruit or silique. As such, seed and fruitdevelopment requires the orchestrated transcription of numerouspolynucleotides, some of which are ubiquitous, others that areembryo-specific and still others that are expressed only in theendosperm, seed coat, or fruit. Such genes are termed fruit developmentresponsive genes and can be used to modulate seed and fruit growth anddevelopment such as seed size, seed yield, seed composition and seeddormancy.

Differential Expression of the Sequences in Siliques, Inflorescences andFlowers

The relative levels of mRNA product in the siliques relative to theplant as a whole was measured.

Differential Expression of the Sequences in Hybrid Seed Development

The levels of mRNA product in the seeds relative to those in a leaf andfloral stems was measured.

Development Genes, Gene Components And Products

Imbibition And Germination Responsive Genes, Gene Components AndProducts

Seeds are a vital component of the world's diet. Cereal grains alone,which comprise ˜90% of all cultivated seeds, contribute up to half ofthe global per capita energy intake. The primary organ system for seedproduction in flowering plants is the ovule. At maturity, the ovuleconsists of a haploid female gametophyte or embryo sac surrounded byseveral layers of maternal tissue including the nucleus and theinteguments. The embryo sac typically contains seven cells including theegg cell, two synergids, a large central cell containing two polarnuclei, and three antipodal cells. That pollination results in thefertilization of both egg and central cell. The fertilized egg developsinto the embryo. The fertilized central cell develops into theendosperm. And the integuments mature into the seed coat. As the ovuledevelops into the seed, the ovary matures into the fruit or silique.Late in development, the developing seed ends a period of extensivebiosynthetic and cellular activity and begins to desiccate to completeits development and enter a dormant, metabolically quiescent state. Seeddormancy is generally an undesirable characteristic in agriculturalcrops, where rapid germination and growth are required. However, somedegree of dormancy is advantageous, at least during seed development.This is particularly true for cereal crops because it preventsgermination of grains while still on the ear of the parent plant(preharvest sprouting), a phenomenon that results in major losses to theagricultural industry. Extensive domestication and breeding of cropspecies have ostensibly reduced the level of dormancy mechanisms presentin the seeds of their wild ancestors, although under some adverseenvironmental conditions, dormancy may reappear. By contrast, weed seedsfrequently mature with inherent dormancy mechanisms that allow someseeds to persist in the soil for many years before completinggermination.

Germination commences with imbibition, the uptake of water by the dryseed, and the activation of the quiescent embryo and endosperm. Theresult is a burst of intense metabolic activity. At the cellular level,the genome is transformed from an inactive state to one of intensetranscriptional activity. Stored lipids, carbohydrates and proteins arecatabolized fueling seedling growth and development. DNA and organellesare repaired, replicated and begin functioning. Cell expansion and celldivision are triggered. The shoot and root apical meristem are activatedand begin growth and organogenesis. Schematic 4 summarizes some of themetabolic and cellular processes that occur during imbibition.Germination is complete when a part of the embryo, the radicle, extendsto penetrate the structures that surround it. In Arabidopsis, seedgermination takes place within twenty-four (24) hours after imbibition.As such, germination requires the rapid and orchestrated transcriptionof numerous polynucleotides. Germination is followed by expansion of thehypocotyl and opening of the cotyledons. Meristem development continuesto promote root growth and shoot growth, which is followed by early leafformation.

Imbibition and Germination Genes

Imbibition and germination includes those events that commence with theuptake of water by the quiescent dry seed and terminate with theexpansion and elongation of the shoots and roots. The germination periodexists from imbibition to when part of the embryo, usually the radicle,extends to penetrate the seed coat that surrounds it. Imbibition andgermination genes are defined as genes, gene components and productscapable of modulating one or more processes of imbibition andgermination described above. They are useful to modulate many planttraits from early vigor to yield to stress tolerance.

Differential Expression of the Sequences in Germinating Seeds andImbibed Embryos

The levels of mRNA product in the seeds versus the plant as a whole wasmeasured.

Hormone Responsive Genes, Gene Components and Products

Abscissic Acid Responsive Genes, Gene Components and Products

Plant hormones are naturally occurring substances, effective in verysmall amounts, which act as signals to stimulate or inhibit growth orregulate developmental processes in plants. Abscisic acid (ABA) is aubiquitous hormone in vascular plants that has been detected in everymajor organ or living tissue from the root to the apical bud. The majorphysiological responses affected by ABA are dormancy, stress stomatalclosure, water uptake, abscission and senescence. In contrast to Auxins,cytokinins and gibberellins, which are principally growth promoters, ABAprimarily acts as an inhibitor of growth and metabolic processes.

Changes in ABA concentration internally or in the surroundingenvironment in contact with a plant results in modulation of many genesand gene products. These genes and/or products are responsible foreffects on traits such as plant vigor and seed yield. While ABAresponsive polynucleotides and gene products can act alone, combinationsof these polynucleotides also affect growth and development. Usefulcombinations include different ABA responsive polynucleotides and/orgene products that have similar transcription profiles or similarbiological activities, and members of the same or similar biochemicalpathways. Whole pathways or segments of pathways are controlled bytranscription factor proteins and proteins controlling the activity ofsignal transduction pathways. Therefore, manipulation of such proteinlevels is especially useful for altering phenotypes and biochemicalactivities of plants. In addition, the combination of an ABA responsivepolynucleotide and/or gene product with another environmentallyresponsive polynucleotide is also useful because of the interactionsthat exist between hormone-regulated pathways, stress and defenseinduced pathways, nutritional pathways and development.

Differential Expression of the Sequences in ABA Treated Plants

The relative levels of mRNA product in plants treated with ABA versuscontrols treated with water were measured.

Brassinosteroid Responsive Genes, Gene Components and Products

Plant hormones are naturally occurring substances, effective in verysmall amounts, which act as signals to stimulate or inhibit growth orregulate developmental processes in plants. Brassinosteroids (BRs) arethe most recently discovered, and least studied, class of planthormones. The major physiological response affected by BRs is thelongitudinal growth of young tissue via cell elongation and possiblycell division. Consequently, disruptions in BR metabolism, perceptionand activity frequently result in a dwarf phenotype. In addition,because BRs are derived from the sterol metabolic pathway, anyperturbations to the sterol pathway can affect the BR pathway. In thesame way, perturbations in the BR pathway can have effects on the laterpart of the sterol pathway and thus the sterol composition of membranes.

Changes in BR concentration in the surrounding environment or in contactwith a plant result in modulation of many genes and gene products. Thesegenes and/or products are responsible for effects on traits such asplant biomass and seed yield. These genes were discovered andcharacterized from a much larger set of genes by experiments designed tofind genes whose mRNA abundance changed in response to application ofBRs to plants.

While BR responsive polynucleotides and gene products can act alone,combinations of these polynucleotides also affect growth anddevelopment. Useful combinations include different BR responsivepolynucleotides and/or gene products that have similar transcriptionprofiles or similar biological activities, and members of the same orfunctionally related biochemical pathways. Whole pathways or segments ofpathways are controlled by transcription factors and proteinscontrolling the activity of signal transduction pathways. Therefore,manipulation of such protein levels is especially useful for alteringphenotypes and biochemical activities of plants. In addition, thecombination of a BR responsive polynucleotide and/or gene product withanother environmentally responsive polynucleotide is useful because ofthe interactions that exist between hormone-regulated pathways, stresspathways, nutritional pathways and development. Here, in addition topolynucleotides having similar transcription profiles and/or biologicalactivities, useful combinations include polynucleotides that may havedifferent transcription profiles but which participate in common oroverlapping pathways.

Differential Expression of the Sequences in Epi-Brassinolide orBrassinozole Plants

The relative levels of mRNA product in plants treated with eitherepi-brassinolide or brassinozole were measured.

Metabolism Affecting Genes, Gene Components and Products

Nitrogen Responsive Genes, Gene Components and Products

Nitrogen is often the rate-limiting element in plant growth, and allfield crops have a fundamental dependence on exogenous nitrogen sources.Nitrogenous fertilizer, which is usually supplied as ammonium nitrate,potassium nitrate, or urea, typically accounts for 40% of the costsassociated with crops, such as corn and wheat in intensive agriculture.Increased efficiency of nitrogen use by plants should enable theproduction of higher yields with existing fertilizer inputs and/orenable existing yields of crops to be obtained with lower fertilizerinput, or better yields on soils of poorer quality. Also, higher amountsof proteins in the crops could also be produced more cost-effectively.“Nitrogen responsive” genes and gene products can be used to alter ormodulate plant growth and development.

Differential Expression of the Sequences in Whole Seedlings, Shoots andRoots

The relative levels of mRNA product in whole seedlings, shoots and rootstreated with either high or low nitrogen media were compared tocontrols.

Viability Genes, Gene Components and Products

Plants contain many proteins and pathways that when blocked or inducedlead to cell, organ or whole plant death. Gene variants that influencethese pathways can have profound effects on plant survival, vigor andperformance. The critical pathways include those concerned withmetabolism and development or protection against stresses, diseases andpests. They also include those involved in apoptosis and necrosis.Viability genes can be modulated to affect cell or plant death.

Herbicides are, by definition, chemicals that cause death of tissues,organs and whole plants. The genes and pathways that are activated orinactivated by herbicides include those that cause cell death as well asthose that function to provide protection.

Differential Expression of the Sequences in Herbicide Treated Plants andHerbicide Resistant Mutants

The relative levels of mRNA product in plants treated with herbicide andmutants resistant to herbicides were compared to control plants.

Stress Responsive Genes, Gene Components and Products

Wounding Responsive Genes, Gene Components and Products

Plants are continuously subjected to various forms of wounding fromphysical attacks including the damage created by pathogens and pests,wind, and contact with other objects. Therefore, survival andagricultural yields depend on constraining the damage created by thewounding process and inducing defense mechanisms against future damage.

Plants have evolved complex systems to minimize and/or repair localdamage and to minimize subsequent attacks by pathogens or pests or theireffects. These involve stimulation of cell division and cell elongationto repair tissues, induction of programmed cell death to isolate thedamage caused mechanically and by invading pests and pathogens, andinduction of long-range signaling systems to induce protectingmolecules, in case of future attack. The genetic and biochemical systemsassociated with responses to wounding are connected with thoseassociated with other stresses such as pathogen attack and drought.

Wounding responsive genes and gene products can be used to alter ormodulate traits such as growth rate; whole plant height, width, orflowering time; organ development (such as coleoptile elongation, youngleaves, roots, lateral roots, tuber formation, flowers, fruit, andseeds); biomass; fresh and dry weight during any time in plant life,such as at maturation; number of flowers; number of seeds; seed yield,number, size, weight, harvest index (such as content and composition,e.g., amino acid, nitrogen, oil, protein, and carbohydrate); fruityield, number, size, weight, harvest index, post harvest quality,content and composition (e.g., amino acid, carotenoid, jasmonate,protein, and starch); seed and fruit development; germination of dormantand non-dormant seeds; seed viability, seed reserve mobilization, fruitripening, initiation of the reproductive cycle from a vegetative state,flower development time, insect attraction for fertilization, time tofruit maturity, senescence; fruits, fruit drop; leaves; stress anddisease responses; drought; heat and cold; wounding by any source,including wind, objects, pests and pathogens; uv and high light damage(insect, fungus, virus, worm, nematode damage).

Cold Responsive Genes, Gene Components and Products

The ability to endure low temperatures and freezing is a majordeterminant of the geographical distribution and productivity ofagricultural crops. Even in areas considered suiTable for thecultivation of a given species or cultivar, can give rise to yielddecreases and crop failures as a result of aberrant, freezingtemperatures. Even modest increases (1-2° C.) in the freezing toleranceof certain crop species would have a dramatic impact on agriculturalproductivity in some areas. The development of genotypes with increasedfreezing tolerance would provide a more reliable means to minimize croplosses and diminish the use of energy-costly practices to modify themicroclimate.

Sudden cold temperatures result in modulation of many genes and geneproducts, including promoters. These genes and/or products areresponsible for effects on traits such as plant vigor and seed yield.

Manipulation of one or more cold responsive gene activities is useful tomodulate growth and development.

Differential Expression of the Sequences in Cold Treated Plants

The relative levels of mRNA product in cold treated plants were comparedto control plants.

Heat Responsive Genes, Gene Components and Products

The ability to endure high temperatures is a major determinant of thegeographical distribution and productivity of agricultural crops.Decreases in yield and crop failure frequently occur as a result ofaberrant, hot conditions even in areas considered suiTable for thecultivation of a given species or cultivar. Only modest increases in theheat tolerance of crop species would have a dramatic impact onagricultural productivity. The development of genotypes with increasedheat tolerance would provide a more reliable means to minimize croplosses and diminish the use of energy-costly practices to modify themicroclimate.

Changes in temperature in the surrounding environment or in a plantmicroclimate results in modulation of many genes and gene products.

Differential Expression of the Sequences in Heat Treated Plants

The relative levels of mRNA product in heat treated plants were comparedto control plants.

Drought Responsive Genes, Gene Components and Products

The ability to endure drought conditions is a major determinant of thegeographical distribution and productivity of agricultural crops.Decreases in yield and crop failure frequently occur as a result ofaberrant, drought conditions even in areas considered suiTable for thecultivation of a given species or cultivar. Only modest increases in thedrought tolerance of crop species would have a dramatic impact onagricultural productivity. The development of genotypes with increaseddrought tolerance would provide a more reliable means to minimize croplosses and diminish the use of energy-costly practices to modify themicroclimate.

Drought conditions in the surrounding environment or within a plant,results in modulation of many genes and gene products.

Differential Expression of the Sequences in Drought Treated Plants andDrought Mutants

The relative levels of mRNA product in drought treated plants anddrought mutants were compared to control plants.

Methyl Jasmonate (Jasmonate) Responsive Genes, Gene Components andProducts

Jasmonic acid and its derivatives, collectively referred to asjasmonates, are naturally occurring derivatives of plant lipids. Thesesubstances are synthesized from linolenic acid in alipoxygenase-dependent biosynthetic pathway. Jasmonates are signallingmolecules which have been shown to be growth regulators as well asregulators of defense and stress responses. As such, jasmonatesrepresent a separate class of plant hormones. Jasmonate responsive genescan be used to modulate plant growth and development.

Differential Expression of the Sequences in Methyl Jasmonate TreatedPlants

The relative levels of mRNA product in methyl jasmonate treated plantswere compared to control plants.

Salicylic Acid Responsive Genes, Gene Components and Products

Plant defense responses can be divided into two groups: constitutive andinduced. Salicylic acid (SA) is a signaling molecule necessary foractivation of the plant induced defense system known as systemicacquired resistance or SAR. This response, which is triggered by priorexposure to avirulent pathogens, is long lasting and provides protectionagainst a broad spectrum of pathogens. Another induced defense system isthe hypersensitive response (HR). HR is far more rapid, occurs at thesites of pathogen (avirulent pathogens) entry and precedes SAR. SA isalso the key signaling molecule for this defense pathway.

Differential Expression of the Sequences in Salicylic Acid TreatedPlants

The relative levels of mRNA product in salicylic acid treated plantswere compared to control plants.

Osmotic Stress Responsive Genes, Gene Components and Products

The ability to endure and recover from osmotic and salt related stressis a major determinant of the geographical distribution and productivityof agricultural crops. Osmotic stress is a major component of stressimposed by saline soil and water deficit. Decreases in yield and cropfailure frequently occur as a result of aberrant or transientenvironmental stress conditions even in areas considered suitable forthe cultivation of a given species or cultivar. Only modest increases inthe osmotic and salt tolerance of a crop species would have a dramaticimpact on agricultural productivity. The development of genotypes withincreased osmotic tolerance would provide a more reliable means tominimize crop losses and diminish the use of energy-costly practices tomodify the soil environment. Thus, osmotic stress responsive genes canbe used to modulate plant growth and development.

Differential Expression of the Sequences in Peg Treated Plants

The relative levels of mRNA product in PEG treated plants were comparedto control plants.

Shade Responsive Genes, Gene Components and Products

Plants sense the ratio of Red (R):Far Red (FR) light in theirenvironment and respond differently to particular ratios. A low R:FRratio, for example, enhances cell elongation and favors flowering overleaf production. The changes in R:FR ratios mimic and cause the shadingresponse effects in plants. The response of a plant to shade in thecanopy structures of agricultural crop fields influences crop yieldssignificantly. Therefore manipulation of genes regulating the shadeavoidance responses can improve crop yields. While phytochromes mediatethe shade avoidance response, the down-stream factors participating inthis pathway are largely unknown. One potential downstream participant,ATHB-2, is a member of the HD-Zip class of transcription factors andshows a strong and rapid response to changes in the R:FR ratio. ATHB-2overexpressors have a thinner root mass, smaller and fewer leaves andlonger hypocotyls and petioles. This elongation arises from longerepidermal and cortical cells, and a decrease in secondary vasculartissues, paralleling the changes observed in wild-type seedlings grownunder conditions simulating canopy shade. On the other hand, plants withreduced ATHB-2 expression have a thick root mass and many larger leavesand shorter hypocotyls and petioles. Here, the changes in the hypocotylresult from shorter epidermal and cortical cells and increasedproliferation of vascular tissue. Interestingly, application of Auxin isable to reverse the root phenotypic consequences of high ATHB-2 levels,restoring the wild-type phenotype. Consequently, given that ATHB-2 istightly regulated by phytochrome, these data suggest that ATHB-2 maylink the Auxin and phytochrome pathways in the shade avoidance responsepathway.

Shade responsive genes can be used to modulate plant growth anddevelopment.

Differential Expression of the Sequences in Far-Red Light Treated Plants

The relative levels of mRNA product in far-red light treated plants werecompared to control plants.

Viability Genes, Gene Components and Products

Plants contain many proteins and pathways that when blocked or inducedlead to cell, organ or whole plant death. Gene variants that influencethese pathways can have profound effects on plant survival, vigor andperformance. The critical pathways include those concerned withmetabolism and development or protection against stresses, diseases andpests. They also include those involved in apoptosis and necrosis. Theapplicants have elucidated many such genes and pathways by discoveringgenes that when inactivated lead to cell or plant death.

Herbicides are, by definition, chemicals that cause death of tissues,organs and whole plants. The genes and pathways that are activated orinactivated by herbicides include those that cause cell death as well asthose that function to provide protection. The applicants haveelucidated these genes.

The genes defined in this section have many uses including manipulatingwhich cells, tissues and organs are selectively killed, which areprotected, making plants resistant to herbicides, discovering newherbicides and making plants resistant to various stresses.

Viability genes were also identified from a much larger set of genes byexperiments designed to find genes whose mRNA products changed inconcentration in response to applications of different herbicides toplants. Viability genes are characteristically differentiallytranscribed in response to fluctuating herbicide levels orconcentrations, whether internal or external to an organism or cell. TheMA_diff Table reports the changes in transcript levels of variousviability genes.

Early Seedling-Phase Specific Responsive Genes, Gene Components andProducts

One of the more active stages of the plant life cycle is a few daysafter germination is complete, also referred to as the early seedlingphase. During this period the plant begins development and growth of thefirst leaves, roots, and other organs not found in the embryo. Generallythis stage begins when germination ends. The first sign that germinationhas been completed is usually that there is an increase in length andfresh weight of the radicle. Such genes and gene products can regulate anumber of plant traits to modulate yield. For example, these genes areactive or potentially active to a greater extent in developing andrapidly growing cells, tissues and organs, as exemplified by developmentand growth of a seedling 3 or 4 days after planting a seed.

Rapid, efficient establishment of a seedling is very important incommercial agriculture and horticulture. It is also vital that resourcesare approximately partitioned between shoot and root to facilitateadaptive growth. Phototropism and geotropism need to be established. Allthese require post-germination process to be sustained to ensure thatvigorous seedlings are produced. Early seedling phase genes, genecomponents and products are useful to manipulate these and otherprocesses.

Guard Cell Genes, Gene Components and Products

Scattered throughout the epidermis of the shoot are minute pores calledstomata. Each stomal pore is surrounded by two guard cells. The guardcells control the size of the stomal pore, which is critical since thestomata control the exchange of carbon dioxide, oxygen, and water vaporbetween the interior of the plant and the outside atmosphere. Stomataopen and close through turgor changes driven by ion fluxes, which occurmainly through the guard cell plasma membrane and tonoplast. Guard cellsare known to respond to a number of external stimuli such as changes inlight intensity, carbon dioxide and water vapor, for example. Guardcells can also sense and rapidly respond to internal stimuli includingchanges in ABA, auxin and calcium ion flux.

Thus, genes, gene products, and fragments thereof differentiallytranscribed and/or translated in guard cells can be useful to modulateABA responses, drought tolerance, respiration, water potential, andwater management as examples. All of which can in turn affect plantyield including seed yield, harvest index, fruit yield, etc.

To identify such guard cell genes, gene products, and fragments thereof,Applicants have performed a microarray experiment comparing thetranscript levels of genes in guard cells versus leaves. Experimentaldata is shown below.

Nitric Oxide Responsive Genes, Gene Components and Products

The rate-limiting element in plant growth and yield is often its abilityto tolerate suboptimal or stress conditions, including pathogen attackconditions, wounding and the presence of various other factors. Tocombat such conditions, plant cells deploy a battery of inducibledefense responses, including synergistic interactions between nitricoxide (NO), reactive oxygen intermediates (ROS), and salicylic acid(SA). NO has been shown to play a critical role in the activation ofinnate immune and inflammatory responses in animals. At least part ofthis mammalian signaling pathway is present in plants, where NO is knownto potentiate the hypersensitive response (HR). In addition, NO is astimulator molecule in plant photomorphogenesis.

Changes in nitric oxide concentration in the internal or surroundingenvironment, or in contact with a plant, results in modulation of manygenes and gene products.

In addition, the combination of a nitric oxide responsive polynucleotideand/or gene product with other environmentally responsivepolynucleotides is also useful because of the interactions that existbetween hormone regulated pathways, stress pathways, pathogen stimulatedpathways, nutritional pathways and development.

Nitric oxide responsive genes and gene products can function either toincrease or dampen the above phenotypes or activities either in responseto changes in nitric oxide concentration or in the absence of nitricoxide fluctuations. More specifically, these genes and gene products canmodulate stress responses in an organism. In plants, these genes andgene products are useful for modulating yield under stress conditions.Measurements of yield include seed yield, seed size, fruit yield, fruitsize, etc.

Shoot-Apical Meristem Genes, Gene Components and Products

New organs, stems, leaves, branches and inflorescences develop from thestem apical meristem (SAM). The growth structure and architecture of theplant therefore depends on the behavior of SAMs. Shoot apical meristems(SAMs) are comprised of a number of morphologically undifferentiated,dividing cells located at the tips of shoots. SAM genes elucidated hereare capable of modifying the activity of SAMs and thereby many traits ofeconomic interest from ornamental leaf shape to organ number toresponses to plant density.

-   -   In addition, a key attribute of the SAM is its capacity for        self-renewal. Thus, SAM genes of the instant invention are        useful for modulating one or more processes of SAM structure        and/or function including (I) cell size and division; (II) cell        differentiation and organ primordia. The genes and gene        components of this invention are useful for modulating any one        or all of these cell division processes generally, as in timing        and rate, for example. In addition, the polynucleotides and        polypeptides of the invention can control the response of these        processes to the internal plant programs associated with        embryogenesis, and hormone responses, for example.

Because SAMs determine the architecture of the plant, modified plantswill be useful in many agricultural, horticultural, forestry and otherindustrial sectors. Plants with a different shape, numbers of flowersand seed and fruits will have altered yields of plant parts. Forexample, plants with more branches can produce more flowers, seed orfruits. Trees without lateral branches will produce long lengths ofclean timber. Plants with greater yields of specific plant parts will beuseful sources of constituent chemicals.

GFP Experimental Procedures and Results

Procedures

The polynucleotide sequences of the present invention were tested forpromoter activity using Green Fluorescent Protein (GFP) assays in thefollowing manner.

Approximately 1-2 kb of genomic sequence occurring immediately upstreamof the ATG translational start site of the gene of interest was isolatedusing appropriate primers tailed with BstXI restriction sites. StandardPCR reactions using these primers and genomic DNA were conducted. Theresulting product was isolated, cleaved with BstXI and cloned into theBstXI site of an appropriate vector, such as pNewBin4-HAP1-GFP (see FIG.1).

Transformation

The following procedure was used for transformation of plants

1. Stratification of WS-2 Seed.

-   -   Add 0.5 ml WS-2 (CS2360) seed to 50 ml of 0.2% Phytagar in a 50        ml Corning tube and vortex until seeds and Phytagar form a        homogenous mixture.    -   Cover tube with foil and stratify at 4° C. for 3 days.        2. Preparation of Seed Mixture.    -   Obtain stratified seed from cooler.    -   Add seed mixture to a 1000 ml beaker.    -   Add an additional 950 ml of 0.2% Phytagar and mix to homogenize.        3. Preparation of Soil Mixture.    -   Mix 24 L SunshineMix #5 soil with 16 L Therm-O-Rock vermiculite        in cement mixer to make a 60:40 soil mixture.    -   Amend soil mixture by adding 2 Tbsp Marathon and 3 Tbsp Osmocote        and mix contents thoroughly.    -   Add 1 Tbsp Peters fertilizer to 3 gallons of water and add to        soil mixture and mix thoroughly.    -   Fill 4-inch pots with soil mixture and round the surface to        create a slight dome.    -   Cover pots with 8-inch squares of nylon netting and fasten using        rubber bands.    -   Place 14 4-inch pots into each no-hole utility flat.        4. Planting.    -   Using a 60 ml syringe, aspirate 35 ml of the seed mixture.    -   Exude 25 drops of the seed mixture onto each pot.    -   Repeat until all pots have been seeded.    -   Place flats on greenhouse bench, cover flat with clear        propagation domes, place 55% shade cloth on top of flats and        subirrigate by adding 1 inch of water to bottom of each flat.        5. Plant Maintenance.    -   3 to 4 days after planting, remove clear lids and shade cloth.    -   Subirrigate flats with water as needed.    -   After 7-10 days, thin pots to 20 plants per pot using forceps.    -   After 2 weeks, subirrigate all plants with Peters fertilizer at        a rate of 1 Tsp per gallon water.    -   When bolts are about 5-10 cm long, clip them between the first        node and the base of stem to induce secondary bolts.    -   6 to 7 days after clipping, perform dipping infiltration.        6. Preparation of Agrobacterium.    -   Add 150 ml fresh YEB to 250 ml centrifuge bottles and cap each        with a foam plug (Identi-Plug).    -   Autoclave for 40 min at 121° C.    -   After cooling to room temperature, uncap and add 0.1 ml each of        carbenicillin, spectinomycin and rifampicin stock solutions to        each culture vessel.    -   Obtain Agrobacterium starter block (96-well block with        Agrobacterium cultures grown to an OD₆₀₀ of approximately 1.0)        and inoculate one culture vessel per construct by transferring 1        ml from appropriate well in the starter block.    -   Cap culture vessels and place on Lab-Line incubator shaker set        at 27° C. and 250 RPM.    -   Remove after Agrobacterium cultures reach an OD₆₀₀ of        approximately 1.0 (about 24 hours), cap culture vessels with        plastic caps, place in Sorvall SLA 1500 rotor and centrifuge at        8000 RPM for 8 min at 4° C.    -   Pour out supernatant and put bottles on ice until ready to use.    -   Add 200 ml Infiltration Media (IM) to each bottle, resuspend        Agrobacterium pellets and store on ice.        7. Dipping Infiltration.    -   Pour resuspended Agrobacterium into 16 oz polypropylene        containers.    -   Invert 4-inch pots and submerge the aerial portion of the plants        into the Agrobacterium suspension and let stand for 5 min.    -   Pour out Agrobacterium suspension into waste bucket while        keeping polypropylene container in place and return the plants        to the upright position.    -   Place 10 covered pots per flat.    -   Fill each flat with 1-inch of water and cover with shade cloth.    -   Keep covered for 24 hr and then remove shade cloth and        polypropylene containers.    -   Resume normal plant maintenance.    -   When plants have finished flowering cover each pot with a ciber        plant sleeve.    -   After plants are completely dry, collect seed and place into 2.0        ml micro tubes and store in 100-place cryogenic boxes.        Recipes:        0.2% Phytagar

2 g Phytagar

1 L nanopure water

-   -   Shake until Phytagar suspended    -   Autoclave 20 min        YEB (for 1 L)

5 g extract of meat

5 g Bacto peptone

1 g yeast extract

5 g sucrose

0.24 g magnesium sulfate

-   -   While stirring, add ingredients, in order, to 900 ml nanopure        water    -   When dissolved, adjust pH to 7.2    -   Fill to 1 L with nanopure water    -   Autoclave 35 min        Infiltration Medium (IM) (for 1 L)

2.2 g MS salts

50 g sucrose

5 ul BAP solution (stock is 2 mg/ml)

-   -   While stirring, add ingredients in order listed to 900 ml        nanopure water    -   When dissolved, adjust pH to 5.8.    -   Volume up to 1 L with nanopure water.    -   Add 0.02% Silwet L-77 just prior to resuspending Agrobacterium

High Throughput Screening—T1 Generation

1. Soil Preparation. Wear gloves at all times.

-   -   In a large container, mix 60% autoclaved SunshineMix #5 with 40%        vermiculite.    -   Add 2.5 Tbsp of Osmocote, and 2.5 Tbsp of 1% granular Marathon        per 25 L of soil.    -   Mix thoroughly.        2. Fill Com-Packs With Soil.    -   Loosely fill D601 Com-Packs level to the rim with the prepared        soil.    -   Place filled pot into utility flat with holes, within a no-hole        utility flat.    -   Repeat as necessary for planting. One flat set should contain 6        pots.        3. Saturate Soil.    -   Evenly water all pots until the soil is saturated and water is        collecting in the bottom of the flats.    -   After the soil is completely saturated, dump out the excess        water.        4. Plant the Seed.        5. Stratify the Seeds.    -   After sowing the seed for all the flats, place them into a dark        4° C. cooler.    -   Keep the flats in the cooler for 2 nights for WS seed. Other        ecotypes may take longer. This cold treatment will help promote        uniform germination of the seed.        6. Remove Flats From Cooler and Cover With Shade Cloth. (Shade        cloth is only needed in the greenhouse)    -   After the appropriate time, remove the flats from the cooler and        place onto growth racks or benches.    -   Cover the entire set of flats with 55% shade cloth. The cloth is        necessary to cut down the light intensity during the delicate        germination period.    -   The cloth and domes should remain on the flats until the        cotyledons have fully expanded. This usually takes about 4-5        days under standard greenhouse conditions.        7. Remove 55% Shade Cloth and Propagation Domes.    -   After the cotyledons have fully expanded, remove both the 55%        shade cloth and propagation domes.        8. Spray Plants With Finale Mixture. Wear gloves and protective        clothing at all times.    -   Prepare working Finale mixture by mixing 3 ml concentrated        Finale in 48 oz of water in the Poly-TEK sprayer.    -   Completely and evenly spray plants with a fine mist of the        Finale mixture.    -   Repeat Finale spraying every 3-4 days until only transformants        remain. (Approximately 3 applications are necessary.)    -   When satisfied that only transformants remain, discontinue        Finale spraying.        9. Weed Out Excess Transformants.    -   Weed out excess transformants such that a maximum number of five        plants per pot exist evenly spaced throughout the pot.

GFP Assay

Tissues are dissected by eye or under magnification using INOX 5 gradeforceps and placed on a slide with water and coversliped. An attempt ismade to record images of observed expression patterns at earliest andlatest stages of development of tissues listed below. Specific tissueswill be preceded with High (H), Medium (M), Low (L) designations.

Flower

pedicel

receptacle

nectary

sepal

petal

filament

anther

pollen

carpel

style

papillae

vascular

epidermis

stomata

trichome

Silique

stigma

style

carpel

septum

placentae

transmitting tissue

vascular

epidermis

stomata

abscission zone

ovule

Ovule Pre-fertilization:

inner integument

outer integument

embryo sac

funiculus

chalaza

micropyle

gametophyte Post-fertilization:

zygote

inner integument

outer integument

seed coat

primordia

chalaza

micropyle

early endosperm

mature endosperm

embryo

Embryo

suspensor

preglobular

globular

heart

torpedo

late

mature

provascular

hypophysis

radicle

cotyledons

hypocotyl

Stem

epidermis

cortex

vascular

xylem

phloem

pith

stomata

trichome

Leaf

petiole

mesophyll

vascular

epidermis

trichome

primordia

stomata

stipule

margin

T1 Mature: These are the T1 plants resulting from independenttransformation events. These are screened between stage 6.50-6.90 (meansthe plant is flowering and that 50-90% of the flowers that the plantwill make have developed) which is 4-6 weeks of age. At this stage themature plant possesses flowers, siliques at all stages of development,and fully expanded leaves. We do not generally differentiate between6.50 and 6.90 in the report but rather just indicate 6.50. The plantsare initially imaged under UV with a Leica Confocal microscope. Thisallows examination of the plants on a global level. If expression ispresent, they are imaged using scanning laser confocal microscopy.

T2 Seedling: Progeny are collected from the T1 plants giving the sameexpression pattern and the progeny (T2) are sterilized and plated onagar-solidified medium containing M&S salts. In the event that there wasno expression in the T1 plants, T2 seeds are planted from all lines. Theseedlings are grown in Percival incubators under continuous light at 22°C. for 10-12 days. Cotyledons, roots, hypocotyls, petioles, leaves, andthe shoot meristem region of individual seedlings were screened untiltwo seedlings were observed to have the same pattern. Generally foundthe same expression pattern was found in the first two seedlings.However, up to 6 seedlings were screened before “no expression pattern”was recorded. All constructs are screened as T2 seedlings even if theydid not have an expression pattern in the T1 generation.

T2 Mature: The T2 mature plants were screened in a similar manner to theT1 plants. The T2 seeds were planted in the greenhouse, exposed toselection and at least one plant screened to confirm the T1 expressionpattern. In instances where there were any subtle changes in expression,multiple plants were examined and the changes noted in the tables.

T3 Seedling: This was done similar to the T2 seedlings except that onlythe plants for which we are trying to confirm the pattern are planted.

Image Data:

Images are collected by scanning laser confocal microscopy. Scannedimages are taken as 2-D optical sections or 3-D images generated bystacking the 2-D optical sections collected in series. All scannedimages are saved as TIFF files by imaging software, edited in AdobePhotoshop, and labeled in Powerpoint specifying organ and specificexpressing tissues.

Instrumentation:

Microscope

Inverted Leica DM IRB

Fluorescence filter blocks:

Blue excitation BP 450-490; long pass emission LP 515.

Green excitation BP 515-560; long pass emission LP 590

Objectives

HC PL FLUOTAR 5×/0.5

HCPL APO 10×/0.4 IMM water/glycerol/oil

HCPL APO 20×/0.7 IMM water/glycerol/oil

HCXL APO 63×/1.2 IMM water/glycerol/oil

Leica TCS SP2 Confocal Scanner

Spectral range of detector optics 400-850 nm.

Variable computer controlled pinhole diameter.

Optical zoom 1-32×.

Four simultaneous detectors:

Three channels for collection of fluorescence or reflected light.

One channel for transmitted light detector.

Laser sources:

Blue Ar 458/5 mW, 476 nm/5 mW, 488 nm/20 mW, 514 nm/20 mW.

Green HeNe 543 nm/1.2 mW

Red HeNe 633 nm/10 mW

Results

The section in Table 1 entitled “The spatial expression of thepromoter-marker-vector” presents the results of the GFP assays asreported by their corresponding cDNA ID number, construct number andline number. Unlike the microarray results, which measure the differencein expression of the endogenous cDNA under various conditions, the GFPdata gives the location of expression that is visible under the imagingparameters. Table 3 summarizes the results of the spatial expressionresults for each promoter.

Explanation of Table 1

Table 1 includes various information about each promoter or promotercontrol element of the invention including the nucleotide sequence, thespatial expression promoted by each promoter, and the correspondingresults from different expression experiments.

TABLE 1 Promoter Sequences and Related Information Promoter YP0396Modulates the gene: PAR-related protein The GenBank description of thegene:: NM_124618 Arabidopsis thaliana photoassimilate-responsive proteinPAR-related protein (At5g52390) mRNA, complete cdsgi|30696178|ref|NM_124618.2|[30696178] The promoter sequence:5′ctaagtaaaataagataaaacatgttatttgaatttgaatatcgtgggatgcgtatttcggtatttgattaaaggtctggaaaccggagctcctataacccgaataaaaatgcataacatgttcttccccaacgaggcgagcgggtcagggcactagggtcattgcaggcagctcataaagtcatgatcatctaggagatcaaattgtatgtcggccttctcaaaattacctctaagaatctcaaacccaatcatagaacctctaaaaagacaaagtcgtcgctttagaatgggttcggtttttggaaccatatttcacgtcaatttaatgtttagtataatttctgaacaacagaattttggatttatttgcacgtatacaaatatctaattaataaggacgactcgtgactatccttacattaagtttcactgtcgaaataacatagtacaatacttgtcgttaatttccacgtctcaagtctataccgtcatttacggagaaagaacatctctgtttttcatccaaactactattctcactttgtctatatatttaaaattaagtaaaaaagactcaatagtccaataaaatgatgaccaaatgagaagatggttttgtgccagattttaggaaaagtgagtcaaggtttcacatctcaaatttgactgcataatcttcgccattaacaacggcattatatatgtcaagccaattttccatgttgcgtacttttctattgaggtgaaaatatgggtttgttgattaatcaaagagtttgcctaactaatataactacgactttttcagtgaccattccatgtaaactctgcttagtgtttcatttgtcaacaatattgtcgttactcattaaatcaaggaaaaatatacaattgtataattttcttatattttaaaattaattttga 3′ccaaaagaacatctttccttcgaattttctttcattaacatttcttttacttgtctccttgtgtcttcacttcacatcacaacATG The promoter was cloned from the organism: Arabidopsisthaliana, Columbia ecotype Alternative nucleotides: Predicted Position(bp) Mismatch Predicted/Experimental 1-1000 None Identities = 1000/1000(100%) The promoter was cloned in the vector: pNewbin4-HAP1-GFP Whencloned into the vector the promoter was operably linked to a marker,which was the type: GFP-ER Promoter-marker vector was testedin: Arabidopsis thaliana, WS ecotype Generation screened: XT1 Mature  XT2 Seedling   T2 Mature   T3 Seedling The spatial expression of thepromoter-marker vector was found observed in and would be useful inexpression in any or all of the following: Flower H sepal H petal Hanther H style Silique H style H ovule Ovule H outer integument H outerintegument L seed coat Leaf H vascular Primary Root H epidermis Observedexpression pattern: T1 mature: High GFP expression in the style, sepals,petals, and anthers in flowers. Expressed in outer integuments of ovuleprimordia through developing seed stages and in remnants of abortedovules. High vasculature expression in leaf T2 seedling: Medium to lowroot epidermal expression at root transition zone decreasing toward roottip. Specific to epidermal cells flanking lateral roots. Misc. promoterinformation:  Bidirectionality: Pass  Exons: Pass   Repeats: No TheCeres cDNA ID of the endogenous coding sequence to the promoter:12646726 cDNA nucleotide sequence:ACTACACCCAAAAGAACATCTTTCCTTCGAATTTTCTTTCAATTAACATTTCTTTTACTTGTCTCCTTGTGTCTTCACTTCACATCACAACATGGCTTTGAAGACAGTTTTCGTAGCTTTTATGATTCTCCTTGCCATCTATTCGCAAACGACGTTTGGGGACGATGTGAAGTGCGAGAATCTGGATGAAAACACGTGTGCCTTCGCGGTCTCGTCCACTGGAAAACGTTGCGTTTTGGAGAAGAGCATGAAGAGGAGCGGGATCGAGGTGTACACATGTCGATCATCGGAGATAGAAGCTAACAAGGTCACAAACATTATTGAATCGGACGAGTGCATTAAAGCGTGTGGTCTAGACCGGAAAGCTTTAGGTATATCTTCGGACGCATTGTTGGAATCTCAGTTCACACATAAACTCTGCTCGGTTAAATGCTTAAACCAATGTCCTAACGTAGTCGATCTCTACTTCAACCTTGCTGCTGGTGAAGGAGTGTATTTACCAAAGCTATGTGAATCACAAGAAGGGAAGTCAAGAAGAGCAATGTCGGAAATTAGGAGCTCGGGAATTGCAATGGACACTCTTGCACCGGTTGGACCAGTCATGTTGGGCGAGATAGCACCTGAGCCGGCTACTTCAATGGACAACATGCCTTACGTGCCGGCACCTTCACCGTATTAATTAAGGCAAGGGAAAATGGAGAGGACACGTATGATATCATGAGTTTTCGACGAGAATAATTAAGAGATTTATGTTTAGTTCGACGGTTTTAGTATTACATCGTTTATTGCGTCCTTATATATATGTACTTCATAAAAACACACCACGACACATTAAGAGATGGTGAAAGTAGGCTGCGTTCTGGTGTAACTTTTACACAAGTAACGTCTTATAATATATATGATTCGAATAAAATGTTGAGTTTTGGTGAAAATATATAATATGTTTCTG Codingsequence:MALKTVFVAFMILLAIYSQTTFGDDVKCENLDENTCAFAVSSTGKRCVLEKSMKRSGIEVYTCRSSEIEANKVTNIIESDECIKACGLDRKALGISSDALLESQFTHKLCSVKCLNQCPNVVDLYFNLAAGEGVYLPKLCESQEGKSRRAMSEIRSSGIAMDTLAPVGPVMLGEIAPEPATSMDNMPYVPAPSPY*Microarray data shows that the coding sequence was expressed in thefollowing experiments, which shows that the promoter would be useful tomodulate expression in situations similar to the following: CDNA_IDSHORT_NAME EXPT_REP_ID IS_UP 12646726 At_Root_Tips 108434 − 12646726At_Drought_Flowers 108473 + 12646726 At_Drought_Flowers 108474 +12646726 At_Shoot_Apices 108479 + 12646726 At_Shoot_Apices 108480 −12646726 At_15mM_NH4NO3_L-to-H_Rosette 108489 + 12646726At_ap2_floral_buds 108501 − 12646726 At_Ler-rhl_Root 108594 − 12646726At_Ler-pi_Ovule 108595 + 12646726 At_100uM_ABA 108609 + 12646726At_100uM_ABA_Mutants 20000069 + 12646726 At_100uM_ABA_Mutants 20000070 +12646726 At_100uM_ABA_Mutants 20000071 + 12646726 At_100uM_ABA_Mutants20000072 + 12646726 At_100uM_ABA_Mutants 20000117 + 12646726At_42deg_Heat 20000173 − 12646726 At_Shoots 20000184 − 12646726 At_Roots20000185 − 12646726 At_Root-Tips-vs-Tops 20000227 − 12646726 At_Siliques20000234 + 12646726 At_Open_Flower 20000265 + 12646726 At_Drought20000267 + 12646726 At_100mM_NaCl 20000268 + 12646726 At_100mM_NaCl20000308 + 12646726 At_Drought 20000436 + 12646726 At_Drought 20000437 +12646726 At_Shoots 20000438 − 12646726 At_1uM_BR-BRZ 20000441 − 12646726At_1uM_BR-BRZ 20000443 − 12646726 At_100uM_ABA 20000453 + 12646726At_42deg_Heat 20000457 + 12646726 At_42deg_Heat 20000458 − 12646726At_Guard_Cells 20000495 − 12646726 At_10percent_PEG 20000527 − 12646726At_100uM_ABA_Mutants 20000573 − 12646726 At_100uM_ABA_Mutants 20000574 −12646726 At_15mM_NH4NO3_L-to-H 20000709 − 12646726 At_Line_Comparisons20001151 + 12646726 At_Line_Comparisons 20001300 + 12646726At_Line_Comparisons 20001307 + 12646726 At_Line_Comparisons 20001309 −12646726 At_Line_Comparisons 20001310 − 12646726 At_Interploidy_Crosses20001316 − 12646726 At_Line_Comparisons 20001448 + 12646726At_Drought_Soil_Dry 20001554 + 12646726 At_Drought_Soil_Dry 20001555 +12646726 At_Drought_Soil_Dry 20001556 + 12646726 At_Interploidy_Crosses20001654 + 12646726 At_Interploidy_Crosses 20001704 + 12646726At_Interploidy_Crosses 20001853 + 12646726 At_Drought_Reproduction20001905 + 12646726 At_Drought_Reproduction 20001906 + 12646726At_Drought_Reproduction 20001910 + 12646726 At_Drought_Reproduction20001911 + 12646726 At_8deg_Cold 20002108 − 12646726 At_8deg_Cold20002109 − The parameters for the microarray experiments listed above byExpt_Rep_ID and Short_Name are as follow below: CDNA_ID SHORT_NAMEEXPT_REP_ID PARAM_NAME VALUE 12646726 At_Root_Tips 108434 Tissue RootTips 12646726 At_Drought_Flowers 108473 Timepoint (hr) 7 d 12646726At_Drought_Flowers 108473 Treatment Drought vs. No Drought 12646726At_Drought_Flowers 108473 Tissue Flower 12646726 At_Drought_Flowers108474 Timepoint (hr) 8 d (1 d-post_re-watering) 12646726At_Drought_Flowers 108474 Treatment Drought vs. No Drought 12646726At_Drought_Flowers 108474 Tissue Flower 12646726 At_Shoot_Apices 108479Plant Line AOD4-4 12646726 At_Shoot_Apices 108479 Treatment None12646726 At_Shoot_Apices 108480 Treatment 1uM BR vs. No Treatment12646726 At_Shoot_Apices 108480 Plant Line Ws-2 12646726At_15mM_NH4NO3_L-to- 108489 Timepoint (hr) 4 H_Rosette 12646726At_15mM_NH4NO3_L-to- 108489 Treatment 15 mM NH4NO3 vs. 30 mM H_RosetteMannitol 12646726 At_15mM_NH4NO3_L-to- 108489 Tissue Rosette H_Rosette12646726 At_ap2_floral_buds 108501 Plant Line ap2 (Ler.) 12646726At_ap2_floral_buds 108501 Tissue Closed Flower 12646726 At_Ler-rhl_Root108594 Plant Line Ler_rhl 12646726 At_Ler-rhl_Root 108594 Tissue Roots12646726 At_Ler-pi_Ovule 108595 Plant Line Ler_pi 12646726At_Ler-pi_Ovule 108595 Tissue Ovules 12646726 At_100uM_ABA 108609Timepoint (hr) 24 12646726 At_100uM_ABA 108609 Treatment 100 uM ABA vs.No Treatment 12646726 At_100uM_ABA 108609 Tissue Aerial 12646726At_100uM_ABA_Mutants 20000069 Timepoint (hr) 6 12646726At_100uM_ABA_Mutants 20000069 Treatment 100 uM ABA vs. No Treatment12646726 At_100uM_ABA_Mutants 20000069 Tissue Aerial 12646726At_100uM_ABA_Mutants 20000069 Plant Line CS23 12646726At_100uM_ABA_Mutants 20000070 Timepoint (hr) 6 12646726At_100uM_ABA_Mutants 20000070 Treatment 100 uM ABA vs. No Treatment12646726 At_100uM_ABA_Mutants 20000070 Tissue Aerial 12646726At_100uM_ABA_Mutants 20000070 Plant Line CS24 12646726At_100uM_ABA_Mutants 20000071 Timepoint (hr) 6 12646726At_100uM_ABA_Mutants 20000071 Treatment 100 uM ABA vs. No Treatment12646726 At_100uM_ABA_Mutants 20000071 Tissue Aerial 12646726At_100uM_ABA_Mutants 20000071 Plant Line CS8104 12646726At_100uM_ABA_Mutants 20000072 Timepoint (hr) 6 12646726At_100uM_ABA_Mutants 20000072 Treatment 100 uM ABA vs. No Treatment12646726 At_100uM_ABA_Mutants 20000072 Tissue Aerial 12646726At_100uM_ABA_Mutants 20000072 Plant Line CS8105 12646726At_100uM_ABA_Mutants 20000117 Timepoint (hr) 6 12646726At_100uM_ABA_Mutants 20000117 Treatment 100 uM ABA vs. No Treatment12646726 At_100uM_ABA_Mutants 20000117 Tissue Aerial 12646726At_100uM_ABA_Mutants 20000117 Plant Line Columbia 12646726 At_42deg_Heat20000173 Timepoint (hr) 6 12646726 At_42deg_Heat 20000173 Age (day) 1412646726 At_42deg_Heat 20000173 Temperature (deg 42 vs. 22 C.) 12646726At_42deg_Heat 20000173 Organism A. thaliana 12646726 At_42deg_Heat20000173 Tissue Aerial 12646726 At_42deg_Heat 20000173 Plant Line WS12646726 At_Shoots 20000184 Age (day) 7 vs. 21 12646726 At_Shoots20000184 Organism A. thaliana 12646726 At_Shoots 20000184 Tissue Shootsvs. Whole Plant 12646726 At_Shoots 20000184 Plant Line WS 12646726At_Roots 20000185 Age (day) 7 vs. 21 12646726 At_Roots 20000185 OrganismA. thaliana 12646726 At_Roots 20000185 Tissue Roots vs. Whole Plant12646726 At_Roots 20000185 Plant Line WS 12646726 At_Root-Tips-vs-Tops20000227 Age (day) 7, 10, 14 12646726 At_Root-Tips-vs-Tops 20000227Organism A. thaliana 12646726 At_Root-Tips-vs-Tops 20000227 Tissue RootTips vs. Root Tops 12646726 At_Root-Tips-vs-Tops 20000227 Plant Line WS12646726 At_Siliques 20000234 Age (day) 21 12646726 At_Siliques 20000234Tissue <5 mm Siliques vs. Whole Plant 12646726 At_Siliques 20000234Organism A. thaliana 12646726 At_Siliques 20000234 Plant Line WS12646726 At_Open_Flower 20000265 Age (day) 21 12646726 At_Open_Flower20000265 Organism A. thaliana 12646726 At_Open_Flower 20000265 TissueClosed Flower vs. Whole Plant 12646726 At_Open_Flower 20000265 PlantLine WS 12646726 At_Drought 20000267 Timepoint (hr) 6 12646726At_Drought 20000267 Age (day) 7 12646726 At_Drought 20000267 Organism A.thaliana 12646726 At_Drought 20000267 Treatment Drought vs. No Drought12646726 At_Drought 20000267 Tissue Whole Plant 12646726 At_Drought20000267 Plant Line WS 12646726 At_100mM_NaCl 20000268 Timepoint (hr) 612646726 At_100mM_NaCl 20000268 Age (day) 14 12646726 At_100mM_NaCl20000268 Treatment 100 mM NaCl vs. No Treatment 12646726 At_100mM_NaCl20000268 Organism A. thaliana 12646726 At_100mM_NaCl 20000268 TissueWhole Plant 12646726 At_100mM_NaCl 20000268 Plant Line WS 12646726At_100mM_NaCl 20000308 Age (day) 17 12646726 At_100mM_NaCl 20000308Timepoint (hr) 72 12646726 At_100mM_NaCl 20000308 Treatment 100 mM NaClvs. No Treatment 12646726 At_100mM_NaCl 20000308 Organism A. thaliana12646726 At_100mM_NaCl 20000308 Tissue Whole Plant 12646726At_100mM_NaCl 20000308 Plant Line WS 12646726 At_Drought 20000436 Age(day) 7 12646726 At_Drought 20000436 Timepoint (hr) 12 12646726At_Drought 20000436 Organism A. thaliana 12646726 At_Drought 20000436Treatment Drought vs. No Drought 12646726 At_Drought 20000436 TissueWhole Plant 12646726 At_Drought 20000436 Plant Line WS 12646726At_Drought 20000437 Age (day) 8 12646726 At_Drought 20000437 Timepoint(hr) 24 12646726 At_Drought 20000437 Organism A. thaliana 12646726At_Drought 20000437 Treatment Drought vs. No Drought 12646726 At_Drought20000437 Tissue Whole Plant 12646726 At_Drought 20000437 Plant Line WS12646726 At_Shoots 20000438 Age (day) 14 vs. 21 12646726 At_Shoots20000438 Organism A. thaliana 12646726 At_Shoots 20000438 Tissue Shootsvs. Whole Plant 12646726 At_Shoots 20000438 Plant Line WS 12646726At_1uM_BR-BRZ 20000441 Treatment 1uM BR vs. No Treatment 12646726At_1uM_BR-BRZ 20000441 Tissue Shoot Apices 12646726 At_1uM_BR-BRZ20000443 Treatment 1 uM BRZ vs. No Treatment 12646726 At_1uM_BR-BRZ20000443 Tissue Shoot Apices 12646726 At_100uM_ABA 20000453 Age (day) 1512646726 At_100uM_ABA 20000453 Timepoint (hr) 24 12646726 At_100uM_ABA20000453 Treatment 100 uM ABA vs. No Treatment 12646726 At_100uM_ABA20000453 Organism A. thaliana 12646726 At_100uM_ABA 20000453 TissueAerial 12646726 At_100uM_ABA 20000453 Plant Line WS 12646726At_42deg_Heat 20000457 Timepoint (hr) 0.166 12646726 At_42deg_Heat20000457 Age (day) 14 12646726 At_42deg_Heat 20000457 Temperature (deg42 vs. 22 C.) 12646726 At_42deg_Heat 20000457 Organism A. thaliana12646726 At_42deg_Heat 20000457 Tissue Aerial 12646726 At_42deg_Heat20000457 Plant Line WS 12646726 At_42deg_Heat 20000458 Timepoint (hr) 812646726 At_42deg_Heat 20000458 Age (day) 14 12646726 At_42deg_Heat20000458 Temperature (deg 42 vs. 22 C.) 12646726 At_42deg_Heat 20000458Organism A. thaliana 12646726 At_42deg_Heat 20000458 Tissue Aerial12646726 At_42deg_Heat 20000458 Plant Line WS 12646726 At_Guard_Cells20000495 Harvest Date 08 Feb. 2002 12646726 At_Guard_Cells 20000495Organism A. thaliana 12646726 At_Guard_Cells 20000495 Tissue Guard Cellsvs. Leaves 12646726 At_10percent_PEG 20000527 Age (day) 20 12646726At_10percent_PEG 20000527 Timepoint (day) 20 12646726 At_10percent_PEG20000527 Treatment 10 percent PEG vs. No Treatment 12646726At_10percent_PEG 20000527 Organism A. thaliana 12646726 At_10percent_PEG20000527 Tissue Whole Plant 12646726 At_10percent_PEG 20000527 PlantLine WS 12646726 At_100uM_ABA_Mutants 20000573 Organism A. thaliana12646726 At_100uM_ABA_Mutants 20000573 Plant Line CS22 vs. Ler wt12646726 At_100uM_ABA_Mutants 20000573 Timepoint (hr) N/A 12646726At_100uM_ABA_Mutants 20000573 Treatment None 12646726At_100uM_ABA_Mutants 20000573 Tissue Whole Plant 12646726At_100uM_ABA_Mutants 20000574 Organism A. thaliana 12646726At_100uM_ABA_Mutants 20000574 Plant Line CS23 vs. Ler wt 12646726At_100uM_ABA_Mutants 20000574 Timepoint (hr) N/A 12646726At_100uM_ABA_Mutants 20000574 Treatment None 12646726At_100uM_ABA_Mutants 20000574 Tissue Whole Plant 12646726At_15mM_NH4NO3_L-to-H 20000709 Timepoint (hr) 4 12646726At_15mM_NH4NO3_L-to-H 20000709 Age (hr) 14 12646726At_15mM_NH4NO3_L-to-H 20000709 Treatment 15 mM NH4NO3 vs. 30 mM Mannitol12646726 At_15mM_NH4NO3_L-to-H 20000709 Organism A. thaliana 12646726At_15mM_NH4NO3_L-to-H 20000709 Tissue Aerial 12646726At_15mM_NH4NO3_L-to-H 20000709 Plant Line WS 12646726At_Line_Comparisons 20001151 Plant Line ME01339-01 vs. WS 12646726At_Line_Comparisons 20001300 Plant Line ME01338-05 vs. WS 12646726At_Line_Comparisons 20001307 Plant Line WBin4-WX2-A vs. WS 12646726At_Line_Comparisons 20001309 Plant Line WBin4-WX49R-A vs. WS 12646726At_Line_Comparisons 20001310 Plant Line WBin4-WX17-A vs. WS 12646726At_Interploidy_Crosses 20001316 Age (day) 5 12646726At_Interploidy_Crosses 20001316 Organism A. thaliana 12646726At_Interploidy_Crosses 20001316 Plant Line Columbia 12646726At_Interploidy_Crosses 20001316 Cross hemi × 2X vs. 2X × 2X 12646726At_Interploidy_Crosses 20001316 Tissue Siliques 12646726At_Line_Comparisons 20001448 Plant Line ME01323-01 vs. WS 12646726At_Drought_Soil_Dry 20001554 Timepoint (day) 7 12646726At_Drought_Soil_Dry 20001554 Age (day) 21 12646726 At_Drought_Soil_Dry20001554 Organism A. thaliana 12646726 At_Drought_Soil_Dry 20001554Treatment Drought vs. No Drought 12646726 At_Drought_Soil_Dry 20001554Post Timepoint (hr) None 12646726 At_Drought_Soil_Dry 20001554Post-Treatment None 12646726 At_Drought_Soil_Dry 20001554 Plant Line WS12646726 At_Drought_Soil_Dry 20001555 Timepoint (day) 10 12646726At_Drought_Soil_Dry 20001555 Age (day) 24 12646726 At_Drought_Soil_Dry20001555 Organism A. thaliana 12646726 At_Drought_Soil_Dry 20001555Treatment Drought vs. No Drought 12646726 At_Drought_Soil_Dry 20001555Post Timepoint (hr) None 12646726 At_Drought_Soil_Dry 20001555Post-Treatment None 12646726 At_Drought_Soil_Dry 20001555 Plant Line WS12646726 At_Drought_Soil_Dry 20001556 Timepoint (day) 12 12646726At_Drought_Soil_Dry 20001556 Age (day) 26 12646726 At_Drought_Soil_Dry20001556 Organism A. thaliana 12646726 At_Drought_Soil_Dry 20001556Treatment Drought vs. No Drought 12646726 At_Drought_Soil_Dry 20001556Post Timepoint (hr) None 12646726 At_Drought_Soil_Dry 20001556Post-Treatment None 12646726 At_Drought_Soil_Dry 20001556 Plant Line WS12646726 At_Interploidy_Crosses 20001654 Age (day) 5 12646726At_Interploidy_Crosses 20001654 Cross 6X × 2X vs. 2X × 2X 12646726At_Interploidy_Crosses 20001654 Organism A. thaliana 12646726At_Interploidy_Crosses 20001654 Plant Line Columbia 12646726At_Interploidy_Crosses 20001654 Tissue Siliques 12646726At_Interploidy_Crosses 20001704 Age (day) 5 12646726At_Interploidy_Crosses 20001704 Cross 4X × 2X vs. 2X × 2X 12646726At_Interploidy_Crosses 20001704 Organism A. thaliana 12646726At_Interploidy_Crosses 20001704 Plant Line Columbia 12646726At_Interploidy_Crosses 20001704 Tissue Siliques 12646726At_Interploidy_Crosses 20001853 Age (day) 5 12646726At_Interploidy_Crosses 20001853 Organism A. thaliana 12646726At_Interploidy_Crosses 20001853 Plant Line Columbia 12646726At_Interploidy_Crosses 20001853 Cross Fis1 vs. 2X × 2X 12646726At_Interploidy_Crosses 20001853 Tissue Siliques 12646726At_Drought_Reproduction 20001905 Timepoint (day) 10 12646726At_Drought_Reproduction 20001905 Age (day) 40 12646726At_Drought_Reproduction 20001905 Organism A. thaliana 12646726At_Drought_Reproduction 20001905 Treatment Drought vs. No Drought12646726 At_Drought_Reproduction 20001905 Tissue Rosettes 12646726At_Drought_Reproduction 20001905 Plant Line WS 12646726At_Drought_Reproduction 20001906 Timepoint (day) 5 12646726At_Drought_Reproduction 20001906 Age (day) 35 12646726At_Drought_Reproduction 20001906 Organism A. thaliana 12646726At_Drought_Reproduction 20001906 Treatment Drought vs. No Drought12646726 At_Drought_Reproduction 20001906 Tissue Siliques 12646726At_Drought_Reproduction 20001906 Plant Line WS 12646726At_Drought_Reproduction 20001910 Timepoint (day) 7 12646726At_Drought_Reproduction 20001910 Age (day) 37 12646726At_Drought_Reproduction 20001910 Organism A. thaliana 12646726At_Drought_Reproduction 20001910 Treatment Drought vs. No Drought12646726 At_Drought_Reproduction 20001910 Tissue Flowers 12646726At_Drought_Reproduction 20001910 Plant Line WS 12646726At_Drought_Reproduction 20001911 Timepoint (day) 10 12646726At_Drought_Reproduction 20001911 Age (day) 40 12646726At_Drought_Reproduction 20001911 Organism A. thaliana 12646726At_Drought_Reproduction 20001911 Treatment Drought vs. No Drought12646726 At_Drought_Reproduction 20001911 Tissue Flowers 12646726At_Drought_Reproduction 20001911 Plant Line WS 12646726 At_8deg_Cold20002108 Age (day) 14 12646726 At_8deg_Cold 20002108 Timepoint (hr) 16812646726 At_8deg_Cold 20002108 Temperature (deg 8 vs. 22 C.) 12646726At_8deg_Cold 20002108 Organism A. thaliana 12646726 At_8deg_Cold20002108 Tissue Whole Plant 12646726 At_8deg_Cold 20002108 Plant Line WS12646726 At_8deg_Cold 20002109 Age (day) 16 12646726 At_8deg_Cold20002109 Timepoint (hr) 216 12646726 At_8deg_Cold 20002109 Temperature(deg 8 vs. 22 C.) 12646726 At_8deg_Cold 20002109 Organism A. thaliana12646726 At_8deg_Cold 20002109 Tissue Whole Plant 12646726 At_8deg_Cold20002109 Plant Line WS Promoter YP0388 Modulates the gene: proteinphosphatase 2C (PP2C), putative The GenBank description of the gene:NM_125312 Arabidopsis thaliana protein phosphatase 2C (PP2C), putative(At5g59220) mRNA, complete cds gi|30697191|ref|NM_125312.2|[30697191]The promoter sequence:5′tatttgtagtgacatattctacaattatcacatttttctcttatgtttcgtagtcgcagatggtcaattttttctataataatttgtccttgaacacaccaaactttagaaacgatgatatataccgtattgtcacgctcacaatgaaacaaacgcgatgaatcgtcatcaccagctaaaagcctaaaacaccatcttagttttcactcagataaaaagattatttgtttccaacctttctattgaattgattagcagtgatgacgtaattagtgatagtttatagtaaaacaaatggaagtggtaataaatttacacaacaaaatatggtaagaatctataaaataagaggttaagagatctcatgttatattaaatgattgaaagaaaaacaaactattggttgatttccatatgtaatagtaagttgtgatgaaagtgatgacgtaattagttgtatttatagtaaaacaaattaaaatggtaaggtaaatttccacaacaaaacttggtaaaaatcttaaaaaaaaaaaaagaggtttagagatcgcatgcgtgtcatcaaaggttctttttcactttaggtctgagtagtgttagactttgattggtgcacgtaagtgtttcgtatcgcgatttaggagaagtacgttttacacgtggacacaatcaacggtcaagatttcgtcgtccagatagaggagcgatacgtcacgccattcaacaatctcctcttcttcattccttcattttgattttgagttttgatctgcccgttcaaaagtctcggtcatctgcccgtaaatataaagatgattatatttatttatatcttctggtgaaagaagctaaTATAaagcttccatggctaatcttgtttaagcttctcttcttcttctctctcctgtgtctcgttcactagttttttttcgggggagagtgatggagtgtgtttgttgaata 3′ cATG The promoter was cloned from theorganism:  Arabidopsis thaliana, Columbia ecotype Alternativenucleotides: Predicted Position (bp) Mismatch Predicted/Experimental1-1000 None Identities = 1000/1000 (100%) The promoter was cloned in thevector: pNewbin4-HAP1-GFP When cloned into the vector the promoter wasoperably linked to a marker, which was the type: GFP-ER Promoter-markervector was tested in: Arabidopsis thaliana, WS ecotype Generationscreened:  XT1 Mature   XT2 Seedling   T2 Mature   T3 Seedling Thespatial expression of the promoter-marker vector was found observed inand would be useful in expression in any or all of the following: FlowerH filament H anther H stomata Silique H ovule Ovule Post-fertilization:H outer H seed coat H chalaza Leaf L vascular H stomata Primary Root Hepidermis Observed expression pattern: T1 mature: Very high GFPexpression levels in stamens of developing flowers. Low expression invasculature of leaves and guard cells throughout plant. High expressionin outer integument of ovules and in seed coats. High incidence ofaborted ovules. T2 seedling: Low expression in root epidermal cells.Misc. promoter information:  Bidirectionality: Pass  Exons:Pass   Repeats: No Optional Promoter Fragments: 5′ UTR region at basepairs 880-987. The Ceres cDNA ID of the endogenous coding sequence tothe promoter: 13593066 cDNA nucleotide sequence:AAAGCTTCCATGGCTAATCTTGTTTAAGCTTCTCTTCTTCTTCTCTCTCCTGTGTCTCGTTCACTAGTTTTTTTTCGGGGGAGAGTGATGGAGTGTGTTTGTTGAATAGTTTTGACGATCACATGGCTGAGATTTGTTACGAGAACGAGACTATGATGATTGAAACGACGGCGACGGTGGTGAAGAAGGCAACGACGACAACGAGGAGACGAGAACGGAGCTCGTCTCAAGCAGCGAGAAGAAGGAGAATGGAGATCCGGAGGTTTAAGTTTGTTTCCGGCGAACAAGAACCTGTCTTCGTCGACGGTGACTTACAGAGGCGGAGGAGAAGAGAATCCACCGTCGCAGCCTCCACCTCCACCGTGTTTTACGAAACGGCGAAGGAAGTTGTCGTCCTATGCGAGTCTCTTAGTTCAACGGTTGTGGCATTGCCTGATCCTGAAGCTTATCCTAAATACGGCGTCGCTTCAGTCTGTGGAAGAAGACGTGAAATGGAAGACGCCGTCGCTGTGCATCCGTTTTTTTCCCGTCATCAGACGGAATATTCATCCACCGGATTTCACTATTGCGGCGTTTACGATGGCCATGGCTGTTCCCATGTAGCGATGAAATGTAGAGAAAGACTACACGAGCTAGTCCGTGAAGAGTTTGAAGCTGATGCTGACTGGGAAAAGTCAATGGCGCGTAGCTTCACGCGCATGGACATGGAGGTTGTTGCGTTGAACGCCGATGGTGCGGCAAAATGCCGGTGCGAGCTTCAGAGGCCGGACTGCGACGCGGTGGGATCCACTGCGGTTGTGTCTGTCCTTACGCCGGAGAAAATCATCGTGGCGAATTGCGGTGACTCACGTGCCGTTCTCTGTCGTAACGGCAAAGCCATTGCTTTATCCTCCGATCATAAGCCAGACCGTCCGGACGAGCTAGACCGGATTCAAGCAGCGGGTGGTCGTGTTATCTACTGGGATGGCCCACGTGTCCTTGGAGTACTTGCAATGTCACGAGCCATTGGAGATAATTACTTGAAGCCGTATGTAATCAGCAGACCGGAGGTAACCGTGACGGACCGGGCCAACGGAGACGATTTTCTTATTCTCGCAAGTGACGGTCTTTGGGACGTTGTTTCAAACGAAACTGCATGTAGCGTCGTTCGAATGTGTTTGAGAGGAAAAGTCAATGGTCAAGTATCATCATCACCGGAAAGGGAAATGACAGGTGTCGGCGCCGGGAATGTGGTGGTTGGAGGAGGAGATTTGCCAGATAAAGCGTGTGAGGAGGCGTCGCTGTTGCTGACGAGGCTTGCGTTGGCTAGACAAAGTTCGGACAACGTAAGTGTTGTGGTGGTTGATCTACGACGAGACACGTAGTTGTATTTGTCTCTCTCGTAATGTTTGTTGTTTTTTGTCCTGAGTCATCGACTTTTGGGCTTTTTCTTTTAACCTTTTTTGCTCTTCGGTGTAAGACAACGAAGGGTTTTTAATTTAGCTTGACTATGGGTTATGTCAGTCACTGTGTTGAATCGCGGTTTAGATCTACAAAGATTTTCACCAGTAGTGAAAATGGTAAAAAGCCGTGAAATGTGAAAGACTTGAGTTCAATTTAATTTTAAATTTAATAGAATCAGTTGATC Coding sequence:MAEICYENETMMIETTATVVKKATTTTRRRERSSSQAARRRRMEIRRFKFVSGEQEPVFVDGDLQRRRRRESTVAASTSTVFYETAKEVVVLCESLSSTVVALPDPEAYPKYGVASVCGRRREMEDAVAVHPFFSRHQTEYSSTGFHYCGVYDGHGCSHVAMKCRERLHELVREEFEADADWEKSMARSFTRMDMEVVALNADGAAKCRCELQRPDCDAVGSTAVVSVLTPEKIIVANCGDSRAVLCRNGKAIALSSDHKPDRPDELDRIQAAGGRVIYWDGPRVLGVLAMSRAIGDNYLKPYVISRPEVTVTDRANGDDFLILASDGLWDVVSNETACSVVRMCLRGKVNGQVSSSPEREMTGVGAGNVVVGGGDLPDKACEEASLLLTRLALARQSSDNVSVVVVDLRRDT* Microarray data shows that the codingsequence was expressed in the following experiments, which shows thatthe promoter would be useful to modulate expression in situationssimilar to the following: CDNA_ID SHORT_NAME EXPT_REP_ID IS_UP 13593066At_100uM_ABA 20000166 + 13593066 At_100uM_ABA 20000169 + 13593066At_2mM_SA 20000182 + 13593066 At_20%_PEG 20000233 + 13593066At_Open_Flower 20000264 − 13593066 At_Drought 20000267 + 13593066At_100mM_NaCl 20000268 + 13593066 At_Pollen 20000326 − 13593066At_Drought 20000436 + 13593066 At_Drought 20000437 + 13593066 At_Shoots20000438 − 13593066 At_100uM_ABA 20000453 + 13593066 At_100uM_ABA20000455 + 13593066 At_100uM_ABA_Mutants 20000576 + 13593066At_Herbicide_Mutants 20000642 − 13593066 At_Line_Comparisons 20001151 +13593066 At_Line_Comparisons 20001184 + 13593066 At_Line_Comparisons20001307 + 13593066 At_Line_Comparisons 20001309 − 13593066At_Line_Comparisons 20001310 − 13593066 At_Far-red-induction 20001451 +13593066 At_Drought_Soil_Dry 20001554 + 13593066 At_Drought_Soil_Dry20001555 + 13593066 At_Drought_Soil_Dry 20001556 + 13593066At_Drought_Soil_Dry 20001557 + 13593066 At_Drought_Soil_Dry 20001559 +13593066 At_Drought_Soil_Dry 20001560 + 13593066 At_50mM_NH4NO3_L-to-H20001757 − 13593066 At_Far-red-enriched-adult 20001771 + 13593066At_Drought_Reproduction 20001904 + 13593066 At_Drought_Reproduction20001905 + 13593066 At_Drought_Reproduction 20001906 + 13593066At_Drought_Reproduction 20001907 + 13593066 At_Drought_Reproduction20001908 + 13593066 At_Drought_Reproduction 20001911 + 13593066At_8deg_Cold 20002107 − 13593066 At_8deg_Cold 20002108 − 13593066At_8deg_Cold 20002109 − 13593066 At_Drought-Air-Dry 20002256 + Theparameters for the microarray experiments listed above by Expt_Rep_IDand Short_Name are as follow below: CDNA_ID SHORT_NAME EXPT_REP_IDPARAM_NAME VALUE 13593066 At_100uM_ABA 20000166 Timepoint (hr) 113593066 At_100uM_ABA 20000166 Age (day) 14 13593066 At_100uM_ABA20000166 Treatment 100 uM ABA vs. No Treatment 13593066 At_100uM_ABA20000166 Organism A. thaliana 13593066 At_100uM_ABA 20000166 TissueAerial 13593066 At_100uM_ABA 20000166 Plant Line WS 13593066At_100uM_ABA 20000169 Timepoint (hr) 6 13593066 At_100uM_ABA 20000169Age (day) 14 13593066 At_100uM_ABA 20000169 Treatment 100 uM ABA vs. NoTreatment 13593066 At_100uM_ABA 20000169 Organism A. thaliana 13593066At_100uM_ABA 20000169 Tissue Aerial 13593066 At_100uM_ABA 20000169 PlantLine WS 13593066 At_2mM_SA 20000182 Timepoint (hr) 6 13593066 At_2mM_SA20000182 Age (day) 14 13593066 At_2mM_SA 20000182 Treatment 2 mM SA vs.No Treatment 13593066 At_2mM_SA 20000182 Organism A. thaliana 13593066At_2mM_SA 20000182 Tissue Aerial 13593066 At_2mM_SA 20000182 Plant LineWS 13593066 At_20%_PEG 20000233 Timepoint (hr) 6 13593066 At_20%_PEG20000233 Treatment 20% PEG vs. No Treatment 13593066 At_20%_PEG 20000233Tissue Aerial 13593066 At_Open_Flower 20000264 Age (day) 21 13593066At_Open_Flower 20000264 Organism A. thaliana 13593066 At_Open_Flower20000264 Tissue Open Flower vs. Whole Plant 13593066 At_Open_Flower20000264 Plant Line WS 13593066 At_Drought 20000267 Timepoint (hr) 613593066 At_Drought 20000267 Age (day) 7 13593066 At_Drought 20000267Organism A. thaliana 13593066 At_Drought 20000267 Treatment Drought vs.No Drought 13593066 At_Drought 20000267 Tissue Whole Plant 13593066At_Drought 20000267 Plant Line WS 13593066 At_100mM_NaCl 20000268Timepoint (hr) 6 13593066 At_100mM_NaCl 20000268 Age (day) 14 13593066At_100mM_NaCl 20000268 Treatment 100 mM NaCl vs. No Treatment 13593066At_100mM_NaCl 20000268 Organism A. thaliana 13593066 At_100mM_NaCl20000268 Tissue Whole Plant 13593066 At_100mM_NaCl 20000268 Plant LineWS 13593066 At_Pollen 20000326 Age (day) 0 vs. 21 13593066 At_Pollen20000326 Organism A. thaliana 13593066 At_Pollen 20000326 Tissue Pollenvs. Whole Plant 13593066 At_Pollen 20000326 Plant Line WS 13593066At_Drought 20000436 Age (day) 7 13593066 At_Drought 20000436 Timepoint(hr) 12 13593066 At_Drought 20000436 Organism A. thaliana 13593066At_Drought 20000436 Treatment Drought vs. No Drought 13593066 At_Drought20000436 Tissue Whole Plant 13593066 At_Drought 20000436 Plant Line WS13593066 At_Drought 20000437 Age (day) 8 13593066 At_Drought 20000437Timepoint (hr) 24 13593066 At_Drought 20000437 Organism A. thaliana13593066 At_Drought 20000437 Treatment Drought vs. No Drought 13593066At_Drought 20000437 Tissue Whole Plant 13593066 At_Drought 20000437Plant Line WS 13593066 At_Shoots 20000438 Age (day) 14 vs. 21 13593066At_Shoots 20000438 Organism A. thaliana 13593066 At_Shoots 20000438Tissue Shoots vs. Whole Plant 13593066 At_Shoots 20000438 Plant Line WS13593066 At_100uM_ABA 20000453 Age (day) 15 13593066 At_100uM_ABA20000453 Timepoint (hr) 24 13593066 At_100uM_ABA 20000453 Treatment 100uM ABA vs. No Treatment 13593066 At_100uM_ABA 20000453 Organism A.thaliana 13593066 At_100uM_ABA 20000453 Tissue Aerial 13593066At_100uM_ABA 20000453 Plant Line WS 13593066 At_100uM_ABA 20000455 Age(day) 16 13593066 At_100uM_ABA 20000455 Timepoint (hr) 48 13593066At_100uM_ABA 20000455 Treatment 100 uM ABA vs. No Treatment 13593066At_100uM_ABA 20000455 Organism A. thaliana 13593066 At_100uM_ABA20000455 Tissue Aerial 13593066 At_100uM_ABA 20000455 Plant Line WS13593066 At_100uM_ABA_Mutants 20000576 Timepoint (hr) 6 13593066At_100uM_ABA_Mutants 20000576 Treatment 1uM ABA vs. No Treatment13593066 At_100uM_ABA_Mutants 20000576 Organism A. thaliana 13593066At_100uM_ABA_Mutants 20000576 Plant Line CS23 13593066At_100uM_ABA_Mutants 20000576 Tissue Whole Plant 13593066At_Herbicide_Mutants 20000642 Timepoint (hr) 12 13593066At_Herbicide_Mutants 20000642 Plant Line 3950BR/PCJE10000 13593066At_Herbicide_Mutants 20000642 Treatment Finale vs. No Treatment 13593066At_Herbicide_Mutants 20000642 Tissue Seedlings 13593066At_Line_Comparisons 20001151 Plant Line ME01339-01 vs. WS 13593066At_Line_Comparisons 20001184 Plant Line ME01848-01 vs. WS 13593066At_Line_Comparisons 20001307 Plant Line WBin4-WX2-A vs. WS 13593066At_Line_Comparisons 20001309 Plant Line WBin4-WX49R-A vs. WS 13593066At_Line_Comparisons 20001310 Plant Line WBin4-WX17-A vs. WS 13593066At_Far-red-induction 20001451 Age (day) 8 13593066 At_Far-red-induction20001451 Timepoint (hr) 24 13593066 At_Far-red-induction 20001451Organism A. thaliana 13593066 At_Far-red-induction 20001451 Plant LineColumbia 13593066 At_Far-red-induction 20001451 Light Far-red vs. White13593066 At_Far-red-induction 20001451 Tissue Whole Plant 13593066At_Drought_Soil_Dry 20001554 Timepoint (day) 7 13593066At_Drought_Soil_Dry 20001554 Age (day) 21 13593066 At_Drought_Soil_Dry20001554 Organism A. thaliana 13593066 At_Drought_Soil_Dry 20001554Treatment Drought vs. No Drought 13593066 At_Drought_Soil_Dry 20001554Post Timepoint (hr) None 13593066 At_Drought_Soil_Dry 20001554Post-Treatment None 13593066 At_Drought_Soil_Dry 20001554 Plant Line WS13593066 At_Drought_Soil_Dry 20001555 Timepoint (day) 10 13593066At_Drought_Soil_Dry 20001555 Age (day) 24 13593066 At_Drought_Soil_Dry20001555 Organism A. thaliana 13593066 At_Drought_Soil_Dry 20001555Treatment Drought vs. No Drought 13593066 At_Drought_Soil_Dry 20001555Post Timepoint (hr) None 13593066 At_Drought_Soil_Dry 20001555Post-Treatment None 13593066 At_Drought_Soil_Dry 20001555 Plant Line WS13593066 At_Drought_Soil_Dry 20001556 Timepoint (day) 12 13593066At_Drought_Soil_Dry 20001556 Age (day) 26 13593066 At_Drought_Soil_Dry20001556 Organism A. thaliana 13593066 At_Drought_Soil_Dry 20001556Treatment Drought vs. No Drought 13593066 At_Drought_Soil_Dry 20001556Post Timepoint (hr) None 13593066 At_Drought_Soil_Dry 20001556Post-Treatment None 13593066 At_Drought_Soil_Dry 20001556 Plant Line WS13593066 At_Drought_Soil_Dry 20001557 Post Timepoint (hr) 3 13593066At_Drought_Soil_Dry 20001557 Timepoint (day) 13 13593066At_Drought_Soil_Dry 20001557 Age (day) 27 13593066 At_Drought_Soil_Dry20001557 Organism A. thaliana 13593066 At_Drought_Soil_Dry 20001557Treatment Drought vs. No Drought 13593066 At_Drought_Soil_Dry 20001557Post-Treatment Re-Water vs. No Drought 13593066 At_Drought_Soil_Dry20001557 Plant Line WS 13593066 At_Drought_Soil_Dry 20001559 Timepoint(day) 14 13593066 At_Drought_Soil_Dry 20001559 Age (day) 28 13593066At_Drought_Soil_Dry 20001559 Post Timepoint (hr) 29 13593066At_Drought_Soil_Dry 20001559 Organism A. thaliana 13593066At_Drought_Soil_Dry 20001559 Treatment Drought vs. No Drought 13593066At_Drought_Soil_Dry 20001559 Post-Treatment Re-Water vs. No Drought13593066 At_Drought_Soil_Dry 20001559 Plant Line WS 13593066At_Drought_Soil_Dry 20001560 Timepoint (day) 14 13593066At_Drought_Soil_Dry 20001560 Age (day) 28 13593066 At_Drought_Soil_Dry20001560 Organism A. thaliana 13593066 At_Drought_Soil_Dry 20001560Treatment Drought vs. No Drought 13593066 At_Drought_Soil_Dry 20001560Post Timepoint (hr) None 13593066 At_Drought_Soil_Dry 20001560Post-Treatment None 13593066 At_Drought_Soil_Dry 20001560 Plant Line WS13593066 At_50mM_NH4NO3_L-to-H 20001757 Timepoint (hr) 6 13593066At_50mM_NH4NO3_L-to-H 20001757 Treatment 50 mM NH4NO3 vs 100 mM Mannitol13593066 At_50mM_NH4NO3_L-to-H 20001757 Tissue Leaf 13593066At_Far-red-enriched-adult 20001771 Timepoint (hr) 16 13593066At_Far-red-enriched-adult 20001771 Age (day) 28 13593066At_Far-red-enriched-adult 20001771 Organism A. thaliana 13593066At_Far-red-enriched-adult 20001771 Tissue Aerial 13593066At_Far-red-enriched-adult 20001771 Plant Line Columbia 13593066At_Far-red-enriched-adult 20001771 Light Far-red enriched vs. White13593066 At_Drought_Reproduction 20001904 Timepoint (day) 7 13593066At_Drought_Reproduction 20001904 Age (day) 37 13593066At_Drought_Reproduction 20001904 Organism A. thaliana 13593066At_Drought_Reproduction 20001904 Treatment Drought vs. No Drought13593066 At_Drought_Reproduction 20001904 Tissue Rosettes 13593066At_Drought_Reproduction 20001904 Plant Line WS 13593066At_Drought_Reproduction 20001905 Timepoint (day) 10 13593066At_Drought_Reproduction 20001905 Age (day) 40 13593066At_Drought_Reproduction 20001905 Organism A. thaliana 13593066At_Drought_Reproduction 20001905 Treatment Drought vs. No Drought13593066 At_Drought_Reproduction 20001905 Tissue Rosettes 13593066At_Drought_Reproduction 20001905 Plant Line WS 13593066At_Drought_Reproduction 20001906 Timepoint (day) 5 13593066At_Drought_Reproduction 20001906 Age (day) 35 13593066At_Drought_Reproduction 20001906 Organism A. thaliana 13593066At_Drought_Reproduction 20001906 Treatment Drought vs. No Drought13593066 At_Drought_Reproduction 20001906 Tissue Siliques 13593066At_Drought_Reproduction 20001906 Plant Line WS 13593066At_Drought_Reproduction 20001907 Timepoint (day) 7 13593066At_Drought_Reproduction 20001907 Age (day) 37 13593066At_Drought_Reproduction 20001907 Organism A. thaliana 13593066At_Drought_Reproduction 20001907 Treatment Drought vs. No Drought13593066 At_Drought_Reproduction 20001907 Tissue Siliques 13593066At_Drought_Reproduction 20001907 Plant Line WS 13593066At_Drought_Reproduction 20001908 Timepoint (day) 10 13593066At_Drought_Reproduction 20001908 Age (day) 40 13593066At_Drought_Reproduction 20001908 Organism A. thaliana 13593066At_Drought_Reproduction 20001908 Treatment Drought vs. No Drought13593066 At_Drought_Reproduction 20001908 Tissue Siliques 13593066At_Drought_Reproduction 20001908 Plant Line WS 13593066At_Drought_Reproduction 20001911 Timepoint (day) 10 13593066At_Drought_Reproduction 20001911 Age (day) 40 13593066At_Drought_Reproduction 20001911 Organism A. thaliana 13593066At_Drought_Reproduction 20001911 Treatment Drought vs. No Drought13593066 At_Drought_Reproduction 20001911 Tissue Flowers 13593066At_Drought_Reproduction 20001911 Plant Line WS 13593066 At_8deg_Cold20002107 Age (day) 11 13593066 At_8deg_Cold 20002107 Timepoint (hr) 9613593066 At_8deg_Cold 20002107 Temperature (deg C.) 8 vs. 22 13593066At_8deg_Cold 20002107 Organism A. thaliana 13593066 At_8deg_Cold20002107 Tissue Whole Plant 13593066 At_8deg_Cold 20002107 Plant Line WS13593066 At_8deg_Cold 20002108 Age (day) 14 13593066 At_8deg_Cold20002108 Timepoint (hr) 168 13593066 At_8deg_Cold 20002108 Temperature(deg C.) 8 vs. 22 13593066 At_8deg_Cold 20002108 Organism A. thaliana13593066 At_8deg_Cold 20002108 Tissue Whole Plant 13593066 At_8deg_Cold20002108 Plant Line WS 13593066 At_8deg_Cold 20002109 Age (day) 1613593066 At_8deg_Cold 20002109 Timepoint (hr) 216 13593066 At_8deg_Cold20002109 Temperature (deg C.) 8 vs. 22 13593066 At_8deg_Cold 20002109Organism A. thaliana 13593066 At_8deg_Cold 20002109 Tissue Whole Plant13593066 At_8deg_Cold 20002109 Plant Line WS 13593066 At_Drought-Air-Dry20002256 Timepoint (hr) 4 13593066 At_Drought-Air-Dry 20002256 Age (day)35 13593066 At_Drought-Air-Dry 20002256 Organism A. thaliana 13593066At_Drought-Air-Dry 20002256 Treatment Drought vs. No Drought 13593066At_Drought-Air-Dry 20002256 Tissue Shoots 13593066 At_Drought-Air-Dry20002256 Plant Line WS Promoter YP0385 Modulates the gene: Neoxanthincleavage enzyme. The GenBank description of the gene: NM_112304Arabidopsis thaliana 9-cis-epoxycarotenoid dioxygenase [neoxanthincleavage enzyme](NC1)(NCED1), putative (At3g14440) mRNA, complete cdsgi|30683162|ref|NM_112304.2|[30683162]. The promoter sequence:5′aaaattccaattattgtgttactctattcttctaaatttgaacactaatagactatgacatatgagtatataatgtgaagtcttaagatattttcatgtgggagatgaataggccaagttggagtctgcaaacaagaagctcttgagccacgacataagccaagttgatgaccgtaattaatgaaactaaatgtgtgtggttatatattagggacccatggccatatacacaatttttgtttctgtcgatagcatgcgtttatatatatttctaaaaaaactaacatatttactggatttgagttcgaatattgacactaatataaactacgtaccaaactacatatgtttatctatatttgattgatcgaagaattctgaactgttttagaaaatttcaatacacttaacttcatcttacaacggtaaaagaaatcaccactagacaaacaatgcctcataatgtctcgaaccctcaaactcaagagtatacattttactagattagagaatttgatatcctcaagttgccaaagaattggaagcttttgttaccaaacttagaaacagaagaagccacaaaaaaagacaaagggagttaaagattgaagtgatgcatttgtctaagtgtgaaaggtctcaagtctcaactttgaaccataataacattactcacactccctttttttttctttttttttcccaaagtaccctttttaattccctctataacccactcactccattccctctttctgtcactgattcaacacgtggccacactgatgggatccacctttcctcttacccacctcccggttTATAtaaacccttcacaacacttcatcgctctcaaaccaactctctcttctctcttctctcctctcttctacaagaagaaaaaaaacagagcctttacacatctcaaaatcgaacttactttaaccacc 3′-aATG The promoter was cloned from theorganism:  Arabidopsis thaliana, Columbia ecotype Alternativenucleotides: Predicted Position (bp) Mismatch Predicted/Experimental 7PCR error or ecotype variant SNP g/— 28 Read error a/a corrected 29 PCRerror or ecotype variant SNP a/— The promoter was cloned in thevector: pNewbin4-HAP1-GFP When cloned into the vector the promoter wasoperably linked to a marker, which was the type: GFP-ER Promoter-markervector was tested in: Arabidopsis thaliana, WS ecotype Generationscreened: XT1 Mature   XT2 Seedling   T2 Mature   T3 Seedling Thespatial expression of the promoter-marker vector was found observed inand would be useful in expression in any or all of the following: FlowerL receptacle Silique L abscission zone Primary Root H epidermis Observedexpression pattern of the promoter-marker vector was in: T1 mature:Expression specific to abscission zone of mature flowers. T2 seedling:Expression in root epidermal cells. Expression rapidly decreases fromroot transition zone to mid root. Misc. promoterinformation:  Bidirectionality: Pass  Exons: Pass   Repeats: No OptionalPromoter Fragments: 5′ UTR region at base pairs 880-999. The Ceres cDNAID of the endogenous coding sequence to the promoter: 12658348 cDNAnucleotide sequence:AAACCAACTCTCTCTTCTCTCTTCTCTCCTCTCTTCTACAAGAAGAAAAAAAACAGAGCCTTTACACATCTCAAAATCGAACTTACTTTAACCACCAAATACTGATTGAACACACTTGAAAAATGGCTTCTTTCACGGCAACGGCTGCGGTTTCTGGGAGATGGCTTGGTGGCAATCATACTCAGCCGCCATTATCGTCTTCTCAAAGCTCCGACTTGAGTTATTGTAGCTCCTTACCTATGGCCAGTCGTGTCACACGTAAGCTCAATGTTTCATCTGCGCTTCACACTCCTCCAGCTCTTCATTTCCCTAAGCAATCATCAAACTCTCCCGCCATTGTTGTTAAGCCCAAAGCCAAAGAATCCAACACTAAACAGATGAATTTGTTCCAGAGAGCGGCGGCGGCAGCGTTGGACGCGGCGGAGGGTTTCCTTGTCAGCCACGAGAAGCTACACCCGCTTCCTAAAACGGCTGATCCTAGTGTTCAGATCGCCGGAAATTTTGCTCCGGTGAATGAACAGCCCGTCCGGCGTAATCTTCCGGTGGTCGGAAAACTTCCCGATTCCATCAAAGGAGTGTATGTGCGCAACGGAGCTAACCCACTTCACGAGCCGGTGACAGGTCACCACTTCTTCGACGGAGACGGTATGGTTCACGCCGTCAAATTCGAACACGGTTCAGCTAGCTACGCTTGCCGGTTTACTCAGACTAACCGGTTTGTTCAGGAACGTCAATTGGGTCGACCGGTTTTCCCCAAAGCCATCGGTGAGCTTCACGGCCACACCGGTATTGCCCGACTCATGCTATTCTACGCCAGAGCTGCAGCCGGTATAGTCGACCCGGCACACGGAACCGGTGTAGCTAACGCCGGTTTGGTCTATTTCAATGGCCGGTTATTGGCTATGTCGGAGGATGATTTACCTTACCAAGTTCAGATCACTCCCAATGGAGATTTAAAAACCGTTGGTCGGTTCGATTTTGATGGACAATTAGAATCCACAATGATTGCCCACCCGAAAGTCGACCCGGAATCCGGTGAACTCTTCGCTTTAAGCTACGACGTCGTTTCAAAGCCTTACCTAAAATACTTCCGATTCTCACCGGACGGAACTAAATCACCGGACGTCGAGATTCAGCTTGATCAGCCAACGATGATGCACGATTTCGCGATTACAGAGAACTTCGTCGTCGTACCTGACCAGCAAGTCGTTTTCAAGCTGCCGGAGATGATCCGCGGTGGGTCTCCGGTGGTTTACGACAAGAACAAGGTCGCAAGATTCGGGATTTTAGACAAATACGCCGAAGATTCATCGAACATTAAGTGGATTGATGCTCCAGATTGCTTCTGCTTCCATCTCTGGAACGCTTGGGAAGAGCCAGAAACAGATGAAGTCGTCGTGATAGGGTCCTGTATGACTCCACCAGACTCAATTTTCAACGAGTCTGACGAGAATCTCAAGAGTGTCCTGTCTGAAATCCGCCTGAATCTCAAAACCGGTGAATCAACTCGCCGTCCGATCATCTCCAACGAAGATCAACAAGTCAACCTCGAAGCAGGGATGGTCAACAGAAACATGCTCGGCCGTAAAACCAAATTCGCTTACTTGGCTTTAGCCGAGCCGTGGCCTAAAGTCTCAGGATTCGCTAAAGTTGATCTCACTACTGGAGAAGTTAAGAAACATCTTTACGGCGATAACCGTTACGGAGGAGAGCCTCTGTTTCTCCCCGGAGAAGGAGGAGAGGAAGACGAAGGATACATCCTCTGTTTCGTTCACGACGAGAAGACATGGAAATCGGAGTTACAGATAGTTAACGCCGTTAGCTTAGAGGTTGAAGCAACGGTTAAACTTCCGTCAAGGGTTCCGTACGGATTTCACGGTACATTCATCGGAGCCGATGATTTGGCGAAGCAGGTCGTGTGAGTTCTTATGTGTAAATACGCACAAAATACATATACGTGATGAAGAAGCTTCTAGAAGGAAAAGAGAGAGCGAGATTTACCAGTGGGATGCTCTGCATATACGTCCCCGGAATCTGCTCCTCTGTTTTTTTTTTTTTGCTCTGTTTCTTGTTTGTTGTTTCTTTTGGGGTGCGGTTTGCTAGTTCCCTTTTTTTTGGGGTCAATCTAGAAATCTGAAAGATTTTGAGGGACCAGCTTGTAGCTTTTGGGCTGTAGGGTAGCCTAGCCGTTCGAGCTCAGCTGGTTTCTGTTATTCTTTCACTTATTGTTCATCGTAATGAGAAGTATATAAAATATTAAACAACAAAGATATGTTTGTATATGTGCATGAATTAAGGAACATTTTTTTT Coding sequence:MASFTATAAVSGRWLGGNHTQPPLSSSQSSDLSYCSSLPMASRVTRKLNVSSALHTPPALHFPKQSSNSPAIVVKPKAKESNTKQMNLFQRAAAAALDAAEGFLVSHEKLHPLPKTADPSVQIAGNFAPVNEQPVRRNLPVVGKLPDSIKGVYVRNGANPLHEPVTGHHFFDGDGMVHAVKFEHGSASYACRFTQTNRFVQERQLGRPVFPKAIGELHGHTGIARLMLFYARAAAGIVDPAHGTGVANAGLVYFNGRLLAMSEDDLPYQVQITPNGDLKTVGRFDFDGQLESTMIAHPKVDPESGELFALSYDVVSKPYLKYFRFSPDGTKSPDVEIQLDQPTMMHDFAITENFVVVPDQQVVFKLPEMIRGGSPVVYDKNKVARFGILDKYAEDSSNIKWIDAPDCFCFHLWNAWEEPETDEVVVIGSCMTPPDSIFNESDENLKSVLSEIRLNLKTGESTRRPIISNEDQQVNLEAGMVNRNMLGRKTKFAYLALAEPWPKVSGFAKVDLTTGEVKKHLYGDNRYGGEPLFLPGEGGEEDEGYILCFVHDEKTWKSELQIVNAVSLEVEATVKLPSRVPYGFHGTFIGADDLAKQVV* Microarray data shows that the coding sequence wasexpressed in the following experiments, which shows that the promoterwould be useful to modulate expression in situations similar to thefollowing: CDNA_ID SHORT_NAME EXPT_REP_ID IS_UP 12658348 At_2mM_SA20000182 + 12658348 At_Siliques 20000235 − 12658348 At_Siliques 20000236− 12658348 At_Open_Flower 20000264 − 12658348 At_Open_Flower 20000265 −12658348 At_Drought 20000267 + 12658348 At_100mM_NaCl 20000268 +12658348 At_Open_Flower 20000286 − 12658348 At_Drought 20000436 +12658348 At_Drought 20000437 + 12658348 At_100uM_ABA 20000453 + 12658348At_Herbicide_Mutants 20000640 − 12658348 At_Line_Comparisons 20001195 −12658348 At_Far-red-induction 20001247 + 12658348 At_Line_Comparisons20001309 − 12658348 At_Line_Comparisons 20001310 − 12658348At_Far-red-induction 20001451 + 12658348 At_Drought_Soil_Dry 20001554 +12658348 At_Drought_Soil_Dry 20001555 + 12658348 At_Drought_Soil_Dry20001560 − 12658348 At_50mM_NH4NO3_L-to-H 20001762 + 12658348At_Drought_Reproduction 20001904 + 12658348 At_Drought_Reproduction20001905 + 12658348 At_Drought_Reproduction 20001906 + 12658348At_Drought_Reproduction 20001907 + 12658348 At_Drought_Reproduction20001908 + 12658348 At_Drought_Reproduction 20001910 + 12658348At_Drought_Reproduction 20001911 + 12658348 At_Line_Comparisons20002008 + 12658348 At_Line_Comparisons 20002010 + 12658348 At_8deg_Cold20002105 + 12658348 At_Drought-Air-Dry 20002253 + 12658348At_Drought-Air-Dry 20002255 + The parameters for the microarrayexperiments listed above by Expt_Rep_ID and Short_Name are as followbelow: CDNA_ID SHORT_NAME EXPT_REP_ID PARAM_NAME VALUE 12658348At_2mM_SA 20000182 Timepoint (hr) 6 12658348 At_2mM_SA 20000182 Age(day) 14 12658348 At_2mM_SA 20000182 Treatment 2 mM SA vs. No Treatment12658348 At_2mM_SA 20000182 Organism A. thaliana 12658348 At_2mM_SA20000182 Tissue Aerial 12658348 At_2mM_SA 20000182 Plant Line WS12658348 At_Siliques 20000235 Age (day) 21 12658348 At_Siliques 20000235Tissue 5-10 mm Siliques vs. Whole Plant 12658348 At_Siliques 20000235Organism A. thaliana 12658348 At_Siliques 20000235 Plant Line WS12658348 At_Siliques 20000236 Age (day) 21 12658348 At_Siliques 20000236Tissue >10 mm Siliques vs. Whole Plant 12658348 At_Siliques 20000236Organism A. thaliana 12658348 At_Siliques 20000236 Plant Line WS12658348 At_Open_Flower 20000264 Age (day) 21 12658348 At_Open_Flower20000264 Organism A. thaliana 12658348 At_Open_Flower 20000264 TissueOpen Flower vs. Whole Plant 12658348 At_Open_Flower 20000264 Plant LineWS 12658348 At_Open_Flower 20000265 Age (day) 21 12658348 At_Open_Flower20000265 Organism A. thaliana 12658348 At_Open_Flower 20000265 TissueClosed Flower vs. Whole Plant 12658348 At_Open_Flower 20000265 PlantLine WS 12658348 At_Drought 20000267 Timepoint (hr) 6 12658348At_Drought 20000267 Age (day) 7 12658348 At_Drought 20000267 Organism A.thaliana 12658348 At_Drought 20000267 Treatment Drought vs. No Drought12658348 At_Drought 20000267 Tissue Whole Plant 12658348 At_Drought20000267 Plant Line WS 12658348 At_100mM_NaCl 20000268 Timepoint (hr) 612658348 At_100mM_NaCl 20000268 Age (day) 14 12658348 At_100mM_NaCl20000268 Treatment 100 mM NaCl vs. No Treatment 12658348 At_100mM_NaCl20000268 Organism A. thaliana 12658348 At_100mM_NaCl 20000268 TissueWhole Plant 12658348 At_100mM_NaCl 20000268 Plant Line WS 12658348At_Open_Flower 20000286 Age (day) 21 12658348 At_Open_Flower 20000286Organism A. thaliana 12658348 At_Open_Flower 20000286 Tissue Half Openvs. Whole Plant 12658348 At_Open_Flower 20000286 Plant Line WS 12658348At_Drought 20000436 Age (day) 7 12658348 At_Drought 20000436 Timepoint(hr) 12 12658348 At_Drought 20000436 Organism A. thaliana 12658348At_Drought 20000436 Treatment Drought vs. No Drought 12658348 At_Drought20000436 Tissue Whole Plant 12658348 At_Drought 20000436 Plant Line WS12658348 At_Drought 20000437 Age (day) 8 12658348 At_Drought 20000437Timepoint (hr) 24 12658348 At_Drought 20000437 Organism A. thaliana12658348 At_Drought 20000437 Treatment Drought vs. No Drought 12658348At_Drought 20000437 Tissue Whole Plant 12658348 At_Drought 20000437Plant Line WS 12658348 At_100uM_ABA 20000453 Age (day) 15 12658348At_100uM_ABA 20000453 Timepoint (hr) 24 12658348 At_100uM_ABA 20000453Treatment 100 uM ABA vs. No Treatment 12658348 At_100uM_ABA 20000453Organism A. thaliana 12658348 At_100uM_ABA 20000453 Tissue Aerial12658348 At_100uM_ABA 20000453 Plant Line WS 12658348At_Herbicide_Mutants 20000640 Timepoint (hr) 12 12658348At_Herbicide_Mutants 20000640 Plant Line 05377RR/BR27173 12658348At_Herbicide_Mutants 20000640 Treatment Roundup vs. No Treatment12658348 At_Herbicide_Mutants 20000640 Tissue Seedlings 12658348At_Line_Comparisons 20001195 Plant Line WBin4-WX14-B vs. WS 12658348At_Far-red-induction 20001247 Timepoint (hr) 1 12658348At_Far-red-induction 20001247 Age (day) 7 12658348 At_Far-red-induction20001247 Organism A. thaliana 12658348 At_Far-red-induction 20001247Plant Line Columbia 12658348 At_Far-red-induction 20001247 Light Far-redvs. White 12658348 At_Far-red-induction 20001247 Tissue Whole Plant12658348 At_Line_Comparisons 20001309 Plant Line WBin4-WX49R-A vs. WS12658348 At_Line_Comparisons 20001310 Plant Line WBin4-WX17-A vs. WS12658348 At_Far-red-induction 20001451 Age (day) 8 12658348At_Far-red-induction 20001451 Timepoint (hr) 24 12658348At_Far-red-induction 20001451 Organism A. thaliana 12658348At_Far-red-induction 20001451 Plant Line Columbia 12658348At_Far-red-induction 20001451 Light Far-red vs. White 12658348At_Far-red-induction 20001451 Tissue Whole Plant 12658348At_Drought_Soil_Dry 20001554 Timepoint (day) 7 12658348At_Drought_Soil_Dry 20001554 Age (day) 21 12658348 At_Drought_Soil_Dry20001554 Organism A. thaliana 12658348 At_Drought_Soil_Dry 20001554Treatment Drought vs. No Drought 12658348 At_Drought_Soil_Dry 20001554Post Timepoint (hr) None 12658348 At_Drought_Soil_Dry 20001554Post-Treatment None 12658348 At_Drought_Soil_Dry 20001554 Plant Line WS12658348 At_Drought_Soil_Dry 20001555 Timepoint (day) 10 12658348At_Drought_Soil_Dry 20001555 Age (day) 24 12658348 At_Drought_Soil_Dry20001555 Organism A. thaliana 12658348 At_Drought_Soil_Dry 20001555Treatment Drought vs. No Drought 12658348 At_Drought_Soil_Dry 20001555Post Timepoint (hr) None 12658348 At_Drought_Soil_Dry 20001555Post-Treatment None 12658348 At_Drought_Soil_Dry 20001555 Plant Line WS12658348 At_Drought_Soil_Dry 20001560 Timepoint (day) 14 12658348At_Drought_Soil_Dry 20001560 Age (day) 28 12658348 At_Drought_Soil_Dry20001560 Organism A. thaliana 12658348 At_Drought_Soil_Dry 20001560Treatment Drought vs. No Drought 12658348 At_Drought_Soil_Dry 20001560Post Timepoint (hr) None 12658348 At_Drought_Soil_Dry 20001560Post-Treatment None 12658348 At_Drought_Soil_Dry 20001560 Plant Line WS12658348 At_50mM_NH4NO3_L-to-H 20001762 Timepoint (hr) 6 12658348At_50mM_NH4NO3_L-to-H 20001762 Treatment 50 mM NH4NO3 vs 100 mM Mannitol12658348 At_50mM_NH4NO3_L-to-H 20001762 Tissue Siliques 12658348At_Drought_Reproduction 20001904 Timepoint (day) 7 12658348At_Drought_Reproduction 20001904 Age (day) 37 12658348At_Drought_Reproduction 20001904 Organism A. thaliana 12658348At_Drought_Reproduction 20001904 Treatment Drought vs. No Drought12658348 At_Drought_Reproduction 20001904 Tissue Rosettes 12658348At_Drought_Reproduction 20001904 Plant Line WS 12658348At_Drought_Reproduction 20001905 Timepoint (day) 10 12658348At_Drought_Reproduction 20001905 Age (day) 40 12658348At_Drought_Reproduction 20001905 Organism A. thaliana 12658348At_Drought_Reproduction 20001905 Treatment Drought vs. No Drought12658348 At_Drought_Reproduction 20001905 Tissue Rosettes 12658348At_Drought_Reproduction 20001905 Plant Line WS 12658348At_Drought_Reproduction 20001906 Timepoint (day) 5 12658348At_Drought_Reproduction 20001906 Age (day) 35 12658348At_Drought_Reproduction 20001906 Organism A. thaliana 12658348At_Drought_Reproduction 20001906 Treatment Drought vs. No Drought12658348 At_Drought_Reproduction 20001906 Tissue Siliques 12658348At_Drought_Reproduction 20001906 Plant Line WS 12658348At_Drought_Reproduction 20001907 Timepoint (day) 7 12658348At_Drought_Reproduction 20001907 Age (day) 37 12658348At_Drought_Reproduction 20001907 Organism A. thaliana 12658348At_Drought_Reproduction 20001907 Treatment Drought vs. No Drought12658348 At_Drought_Reproduction 20001907 Tissue Siliques 12658348At_Drought_Reproduction 20001907 Plant Line WS 12658348At_Drought_Reproduction 20001908 Timepoint (day) 10 12658348At_Drought_Reproduction 20001908 Age (day) 40 12658348At_Drought_Reproduction 20001908 Organism A. thaliana 12658348At_Drought_Reproduction 20001908 Treatment Drought vs. No Drought12658348 At_Drought_Reproduction 20001908 Tissue Siliques 12658348At_Drought_Reproduction 20001908 Plant Line WS 12658348At_Drought_Reproduction 20001910 Timepoint (day) 7 12658348At_Drought_Reproduction 20001910 Age (day) 37 12658348At_Drought_Reproduction 20001910 Organism A. thaliana 12658348At_Drought_Reproduction 20001910 Treatment Drought vs. No Drought12658348 At_Drought_Reproduction 20001910 Tissue Flowers 12658348At_Drought_Reproduction 20001910 Plant Line WS 12658348At_Drought_Reproduction 20001911 Timepoint (day) 10 12658348At_Drought_Reproduction 20001911 Age (day) 40 12658348At_Drought_Reproduction 20001911 Organism A. thaliana 12658348At_Drought_Reproduction 20001911 Treatment Drought vs. No Drought12658348 At_Drought_Reproduction 20001911 Tissue Flowers 12658348At_Drought_Reproduction 20001911 Plant Line WS 12658348At_Line_Comparisons 20002008 Plant Line ME03766 vs. WS 12658348At_Line_Comparisons 20002010 Plant Line ME02031 vs. WS 12658348At_8deg_Cold 20002105 Age (day) 7 12658348 At_8deg_Cold 20002105Timepoint (hr) 8 12658348 At_8deg_Cold 20002105 Temperature (deg C.) 8vs. 22 12658348 At_8deg_Cold 20002105 Organism A. thaliana 12658348At_8deg_Cold 20002105 Tissue Whole Plant 12658348 At_8deg_Cold 20002105Plant Line WS 12658348 At_Drought-Air-Dry 20002253 Timepoint (hr) 112658348 At_Drought-Air-Dry 20002253 Age (day) 35 12658348At_Drought-Air-Dry 20002253 Organism A. thaliana 12658348At_Drought-Air-Dry 20002253 Treatment Drought vs. No Drought 12658348At_Drought-Air-Dry 20002253 Tissue Roots 12658348 At_Drought-Air-Dry20002253 Plant Line WS 12658348 At_Drought-Air-Dry 20002255 Timepoint(hr) 1 12658348 At_Drought-Air-Dry 20002255 Age (day) 35 12658348At_Drought-Air-Dry 20002255 Organism A. thaliana 12658348At_Drought-Air-Dry 20002255 Treatment Drought vs. No Drought 12658348At_Drought-Air-Dry 20002255 Tissue Shoots 12658348 At_Drought-Air-Dry20002255 Plant Line WS Promoter YP0384 Modulates the gene: Heat shocktranscription factor family. The GenBank description of the gene:NM_113182 Arabidopsis thaliana heat shock transcription factor family(At3g22830) mRNA, complete cds gi|18403537|ref|NM_113182.1|[18403537]The promoter sequence:5′ataaaaattcacatttgcaaattttattcagtcggaatatatatttgaaacaagttttgaaatccattggacgattaaaattcattgttgagaggataaatatggatttgttcatctgaaccatgtcgttgattagtgattgactaccatgaaaaatatgttatgaaaagtataacaacttttgataaatcacatttattaacaataaatcaagacaaaatatgtcaacaataatagtagtagaagatattaattcaaattcatccgtaacaacaaaaaatcataccacaattaagtgtacagaaaaaccttttggatatatttattgtcgcttttcaatgattttcgtgaaaaggatatatttgtgtaaaataagaaggatcttgacgggtgtaaaaacatgcacaattcttaatttagaccaatcagaagacaacacgaacacttctttattataagctattaaacaaaatcttgcctattttgcttagaataatatgaagagtgactcatcagggagtggaaaatatctcaggatttgcttttagctctaacatgtcaaactatctagatgccaacaacacaaagtgcaaattcttttaatatgaaaacaacaataatatttctaatagaaaattaaaaagggaaataaaatatttttttaaaatatacaaaagaagaaggaatccatcatcaaagttttataaaattgtaatataatacaaacttgtttgcttccttgtctctccctctgtctctctcatctctcctatcttctccatatatacttcatcttcacacccaaaactccacacaaaatatctctccctctatctgcaaattttccaaagttgcatcctttcaatttccactcctctctaaTATAattcacattttcccactattgctgattcatttttttttgtgaattatttcaaacccacataaaa 3′-TG The promoter was cloned from theorganism:  Arabidopsis thaliana, Columbia ecotype Alternativenucleotides: Predicted Position (bp) Mismatch Predicted/Experimental 18SNP c/— The promoter was cloned in the vector: pNewbin4-HAP1-GFP Whencloned into the vector the promoter was operably linked to a marker,which was the type: GFP-ER Promoter-marker vector was tested in:Arabidopsis thaliana, WS ecotype Generation screened: XT1 Mature XT2Seedling T2 Mature T3 Seedling The spatial expression of thepromoter-marker vector was found observed in and would be useful inexpression in any or all of the following: Primary Root H epidermis Htrichoblast H atrichoblast Observed expression pattern of thepromoter-marker vector was in: T1 mature: No expression. T2 seedling:High expression throughout root epidermal cells. Misc. promoterinformation: Bidirectionality: Pass Exons: Pass    Repeats: No OptionalPromoter Fragments: 5′ UTR region at base pairs 839-999. The Ceres cDNAID of the endogenous coding sequence to the promoter: 12730108 cDNAnucleotide sequence:ACAAAATATCTCTCCCTCTATCTGCAAATTTTCCAAAGTTGCATCCTTTCAATTTCCACTCCTCTCTAATATAATTCACATTTTCCCACTATTGCTGATTCATTTTTTTTTGTGAATTATTTCAAACCCACATAAAAAAATCTTTGTTTAAATTTAAAACCATGGATCCTTCATTTAGGTTCATTAAAGAGGAGTTTCCTGCTGGATTCAGTGATTCTCCATCACCACCATCTTCTTCTTCATACCTTTATTCATCTTCCATGGCTGAAGCAGCCATAAATGATCCAACAACATTGAGCTATCCACAACCATTAGAAGGTCTCCATGAATCAGGGCCACCTCCATTTTTGACAAAGACATATGACTTGGTGGAAGATTCAAGAACCAATCATGTCGTGTCTTGGAGCAAATCCAATAACAGCTTCATTGTCTGGGATCCACAGGCCTTTTCTGTAACTCTCCTTCCCAGATTCTTCAAGCACAATAACTTCTCCAGTTTTGTCCGCCAGCTCAACACATATGGTTTCAGAAAGGTGAATCCGGATCGGTGGGAGTTTGCAAACGAAGGGTTTCTTAGAGGGCAAAAGCATCTCCTCAAGAACATAAGGAGAAGAAAAACAAGTAATAATAGTAATCAAATGCAACAACCTCAAAGTTCTGAACAACAATCTCTAGACAATTTTTGCATAGAAGTGGGTAGGTACGGTCTAGATGGAGAGATGGACAGCCTAAGGCGAGACAAGCAAGTGTTGATGATGGAGCTAGTGAGACTAAGACAGCAACAACAAAGCACCAAAATGTATCTCACATTGATTGAAGAGAAGCTCAAGAAGACCGAGTCAAAACAAAAACAAATGATGAGCTTCCTTGCCCGCGCAATGCAGAATCCAGATTTTATTCAGCAGCTAGTAGAGCAGAAGGAAAAGAGGAAAGAGATCGAAGAGGCGATCAGCAAGAAGAGACAAAGACCGATCGATCAAGGAAAAAGAAATGTGGAAGATTATGGTGATGAAAGTGGTTATGGGAATGATGTTGCAGCCTCATCCTCAGCATTGATTGGTATGAGTCAGGAATATACATATGGAAACATGTCTGAATTCGAGATGTCGGAGTTGGACAAACTTGCTATGCACATTCAAGGACTTGGAGATAATTCCAGTGCTAGGGAAGAAGTCTTGAATGTGGAAAAAGGAAATGATGAGGAAGAAGTAGAAGATCAACAACAAGGGTACCATAAGGAGAACAATGAGATTTATGGTGAAGGTTTTTGGGAAGATTTGTTAAATGAAGGTCAAAATTTTGATTTTGAAGGAGATCAAGAAAATGTTGATGTGTTAATTCAGCAACTTGGTTATTTGGGTTCTAGTTCACACACTAATTAAGAAGAAATTGAAATGATGACTACTTTAAGCATTTGAATCAACTTGTTTCCTATTAGTAATTTGGCTTTGTTTCAATCAAGTGAGTCGTGGACTAACTTATTGAATTTGGGGGTTAAATCCGTTTCTTATTTTTGGAAATAAAATTGCTTTTTGTTT Coding sequence:MDPSFRFIKEEFPAGFSDSPSPPSSSSYLYSSSMAEAAINDPTTLSYPQPLEGLHESGPPPFLTKTYDLVEDSRTNHVVSWSKSNNSFIVWDPQAFSVTLLPRFFKHNNFSSFVRQLNTYGFRKVNPDRWEFANEGFLRGQKHLLKNIRRRKTSNNSNQMQQPQSSEQQSLDNFCIEVGRYGLDGEMDSLRRDKQVLMMELVRLRQQQQSTKMYLTLIEEKLKKTESKQKQMMSFLARAMQNPDFIQQLVEQKEKRKEIEEAISKKRQRPIDQGKRNVEDYGDESGYGNDVAASSSALIGMSQEYTYGNMSEFEMSELDKLAMHIQGLGDNSSAREEVLNVEKGNDEEEVEDQQQGYHKENNEIYGEGFWEDLLNEGQNFDFEGDQENVDVLIQQLGYLGSSSHTN* Microarray data shows that the coding sequence wasexpressed in the following experiments, which shows that the promoterwould be useful to modulate expression in situations similar to thefollowing: CDNA_ID SHORT_NAME EXPT_REP_ID IS_UP 12730108 At_Drought20000267 + 12730108 At_100mM_NaCl 20000268 + 12730108 At_Drought20000288 + 12730108 At_Drought 20000436 + 12730108 At_Drought 20000437 +12730108 At_Guard_Cells 20000495 − 12730108 At_Herbicide_Mutants20000639 − 12730108 At_Herbicide_Mutants 20000641 − 12730108At_Drought_Reproduction 20001904 + 12730108 At_Drought_Reproduction20001905 + 12730108 At_Drought_Reproduction 20001911 + 12730108At_Drought-Air-Dry 20002254 + The parameters for the microarrayexperiments listed above by Expt_Rep_ID and Short_Name are as followbelow: CDNA_ID SHORT_NAME EXPT_REP_ID PARAM_NAME VALUE 12730108At_Drought 20000267 Timepoint (hr) 6 12730108 At_Drought 20000267 Age(day) 7 12730108 At_Drought 20000267 Organism A. thaliana 12730108At_Drought 20000267 Treatment Drought vs. No Drought 12730108 At_Drought20000267 Tissue Whole Plant 12730108 At_Drought 20000267 Plant Line WS12730108 At_100mM_NaCl 20000268 Timepoint (hr) 6 12730108 At_100mM_NaCl20000268 Age (day) 14 12730108 At_100mM_NaCl 20000268 Treatment 100 mMNaCl vs. No Treatment 12730108 At_100mM_NaCl 20000268 Organism A.thaliana 12730108 At_100mM_NaCl 20000268 Tissue Whole Plant 12730108At_100mM_NaCl 20000268 Plant Line WS 12730108 At_Drought 20000288Timepoint (hr) 1 12730108 At_Drought 20000288 Age (day) 7 12730108At_Drought 20000288 Organism A. thaliana 12730108 At_Drought 20000288Treatment Drought vs. No Drought 12730108 At_Drought 20000288 TissueWhole Plant 12730108 At_Drought 20000288 Plant Line WS 12730108At_Drought 20000436 Age (day) 7 12730108 At_Drought 20000436 Timepoint(hr) 12 12730108 At_Drought 20000436 Organism A. thaliana 12730108At_Drought 20000436 Treatment Drought vs. No Drought 12730108 At_Drought20000436 Tissue Whole Plant 12730108 At_Drought 20000436 Plant Line WS12730108 At_Drought 20000437 Age (day) 8 12730108 At_Drought 20000437Timepoint (hr) 24 12730108 At_Drought 20000437 Organism A. thaliana12730108 At_Drought 20000437 Treatment Drought vs. No Drought 12730108At_Drought 20000437 Tissue Whole Plant 12730108 At_Drought 20000437Plant Line WS 12730108 At_Guard_Cells 20000495 Harvest Date 08 Feb. 200212730108 At_Guard_Cells 20000495 Organism A. thaliana 12730108At_Guard_Cells 20000495 Tissue Guard Cells vs. Leaves 12730108At_Herbicide_Mutants 20000639 Timepoint (hr) 4 12730108At_Herbicide_Mutants 20000639 Plant Line 05377RR/BR27173 12730108At_Herbicide_Mutants 20000639 Treatment Roundup vs. No Treatment12730108 At_Herbicide_Mutants 20000639 Tissue Seedlings 12730108At_Herbicide_Mutants 20000641 Timepoint (hr) 4 12730108At_Herbicide_Mutants 20000641 Plant Line 3950BR/PCJE10000 12730108At_Herbicide_Mutants 20000641 Treatment Finale vs. No Treatment 12730108At_Herbicide_Mutants 20000641 Tissue Seedlings 12730108At_Drought_Reproduction 20001904 Timepoint (day) 7 12730108At_Drought_Reproduction 20001904 Age (day) 37 12730108At_Drought_Reproduction 20001904 Organism A. thaliana 12730108At_Drought_Reproduction 20001904 Treatment Drought vs. No Drought12730108 At_Drought_Reproduction 20001904 Tissue Rosettes 12730108At_Drought_Reproduction 20001904 Plant Line WS 12730108At_Drought_Reproduction 20001905 Timepoint (day) 10 12730108At_Drought_Reproduction 20001905 Age (day) 40 12730108At_Drought_Reproduction 20001905 Organism A. thaliana 12730108At_Drought_Reproduction 20001905 Treatment Drought vs. No Drought12730108 At_Drought_Reproduction 20001905 Tissue Rosettes 12730108At_Drought_Reproduction 20001905 Plant Line WS 12730108At_Drought_Reproduction 20001911 Timepoint (day) 10 12730108At_Drought_Reproduction 20001911 Age (day) 40 12730108At_Drought_Reproduction 20001911 Organism A. thaliana 12730108At_Drought_Reproduction 20001911 Treatment Drought vs. No Drought12730108 At_Drought_Reproduction 20001911 Tissue Flowers 12730108At_Drought_Reproduction 20001911 Plant Line WS 12730108At_Drought-Air-Dry 20002254 Timepoint (hr) 4 12730108 At_Drought-Air-Dry20002254 Age (day) 35 12730108 At_Drought-Air-Dry 20002254 Organism A.thaliana 12730108 At_Drought-Air-Dry 20002254 Treatment Drought vs. NoDrought 12730108 At_Drought-Air-Dry 20002254 Tissue Roots 12730108At_Drought-Air-Dry 20002254 Plant Line WS Promoter YP0382 Modulates thegene: product = “expressed protein” The GenBank description of the gene:NM_129727 Arabidopsis thaliana expressed protein (At2g41640) mRNA,complete cds gi|30688728|ref|NM_129727.2|[30688728] The promotersequence:5′ttttttaaaattcgttggaacttggaagggattttaaatattattttgttttccttcatttttataggttaataattgtcaaagatacaactcgatggaccaaaataaaataataaaattcgtcgaatttggtaaagcaaaacggtcgaggatagctaatatttatgcgaaacccgttgtcaaagcagatgttcagcgtcacgcacatgccgcaaaaagaatatacatcaacctcttttgaacttcacgccgttttttaggcccacaataatgctacgtcgtcttctgggttcaccctcgttttttttttaaacttctaaccgataaaataaatggtccactatttcttttcttctctgtgtattgtcgtcagagatggtttaaaagttgaaccgaactataacgattctcttaaaatctgaaaaccaaactgaccgattttcttaactgaaaaaaaaaaaaaaaaaaactgaatttaggccaacttgttgtaatatcacaaagaaaattctacaatttaattcatttaaaaataaagaaaaatttaggtaacaatttaactaagtggtctatctaaatcttgcaaattctttgactttgaccaaacacaacttaagttgacagccgtctcctctctgttgtttccgtgttattaccgaaatatcagaggaaagtccactaaaccccaaatattaaaaatagaaacattactttctttacaaaaggaatctaaattgatccctttcattcgtttcactcgtttcatatagttgtatgtatatatgcgtatgcatcaaaaagtctcttTATAtcctcagagtcacccaatcttatctctctctccttcgtcctcaagaaaagtaattctctgtttgtgtagttttctttaccggtgaattttctcttcgttttgtgcttcaaacgtcacccaaatcaccaagatcgatcaa 3′-TG The promoter was cloned from theorganism:  Arabidopsis thaliana, Columbia ecotype Alternativenucleotides: Predicted Position (bp) Mismatch Predicted/Experimental 484Sequence resolution a/— The promoter was cloned in thevector: pNewbin4-HAP1-GFP When cloned into the vector the promoter wasoperably linked to a marker, which was the type: GFP-ER Promoter-markervector was tested in: Arabidopsis thaliana, WS ecotype Generationscreened: XT1 Mature XT2 Seedling T2 Mature T3 Seedling The spatialexpression of the promoter-marker vector was found observed in and wouldbe useful in expression in any or all of the following: Flower H nectaryM sepal M vascular Primary Root H epidermis H root cap Observedexpression pattern: T1 mature: Expressed in nectary glands of flowersand vasculature of sepals (see Report 129. Table 1.B.). T2 seedling:High root epidermal expression through to root cap. Misc. promoterinformation: Bidirectionality: Pass Exons: Pass   Repeats: No OptionalPromoter Fragments: 5′ UTR region at base pairs 842-999. The Ceres cDNAID of the endogenous coding sequence to the promoter: 12735575 cDNAnucleotide sequence:AGAGTCACCCAATCTTATCTCTCTCTCCTTCGTCCTCAAGAAAAGTAATTCTCTGTTTGTGTAGTTTTCTTTACCGGTGAATTTTCTCTTCGTTTTGTGCTTCAAACGTCACCCAAATCACCAAGATCGATCAAAATCGAAACTTAACGTTTCAGAAGATGGTGCAGTACCAGAGATTAATCATCCACCATGGAAGAAAAGAAGATAAGTTTAGAGTTTCTTCAGCAGAGGAAAGTGGTGGAGGTGGTTGTTGCTACTCCAAGAGAGCTAAACAAAAGTTTCGTTGTCTTCTCTTTCTCTCTATCCTCTCTTGCTGTTTCGTCTTGTCTCCTTATTACCTCTTCGGCTTCTCTACTCTCTCCCTCCTAGATTCGTTTCGCAGAGAAATCGAAGGTCTTAGCTCTTATGAGCCAGTTATTACCCCTCTGTGCTCAGAAATCTCCAATGGAACCATTTGTTGTGACAGAACCGGTTTGAGATCTGATATTTGTGTAATGAAAGGTGATGTTCGAACAAACTCTGCTTCTTCCTCAATCTTCCTCTTCACCTCCTCCACCAATAACAACACAAAACCGGAAAAGATCAAACCTTACACTAGAAAATGGGAGACTAGTGTGATGGACACCGTTCAAGAACTCAACCTCATCACCAAAGATTCCAACAAATCTTCAGATCGTGTATGCGATGTGTACCATGATGTTCCTGCTGTGTTCTTCTCCACTGGTGGATACACCGGTAACGTATACCACGAGTTTAACGACGGGATTATCCCTTTGTTTATAACTTCACAGCATTACAACAAAAAAGTTGTGTTTGTGATCGTCGAGTATCATGACTGGTGGGAGATGAAGTATGGAGATGTCGTTTCGCAGCTCTCGGATTATCCTCTGGTTGATTTCAATGGAGATACGAGAACACATTGTTTCAAAGAAGCAACCGTTGGATTACGTATTCACGACGAGTTAACTGTGAATTCTTCTTTGGTCATTGGGAATCAAACCATTGTTGACTTCAGAAACGTTTTGGATAGGGGTTACTCGCATCGTATCCAAAGCTTGACTCAGGAGGAAACAGAGGCGAACGTGACCGCACTCGATTTCAAGAAGAAGCCAAAACTGGTGATTCTTTCAAGAAACGGGTCATCAAGGGCGATATTAAACGAGAATCTTCTCGTGGAGCTAGCAGAGAAAACAGGGTTCAATGTGGAGGTTCTAAGACCACAAAAGACAACGGAAATGGCCAAGATTTATCGTTCGTTGAACACGAGCGATGTAATGATCGGTGTACATGGAGCAGCAATGACTCATTTCCTTTTCTTGAAACCGAAAACCGTTTTCATTCAGATCATCCCATTAGGGACGGACTGGGCGGCAGAGACATATTATGGAGAACCGGCGAAGAAGCTAGGATTGAAGTACGTTGGTTACAAGATTGCGCCGAAAGAGAGCTCTTTGTATGAAGAATATGGGAAAGATGACCCTGTAATCCGAGATCCGGATAGTCTAAACGACAAAGGATGGGAATATACGAAGAAAATCTATCTACAAGGACAGAACGTGAAGCTTGACTTGAGAAGATTCAGAGAAACGTTAACTCGTTCGTATGATTTCTCCATTAGAAGGAGATTTAGAGAAGATTACTTGTTACATAGAGAAGATTAAGAATCGTGTGATATTTTTTTTGTAAAGTTTTGAATGACAATTAAATTTATTTATTTTAT Coding sequence:MVQYQRLIIHHGRKEDKFRVSSAEESGGGGCCYSKRAKQKFRCLLFLSILSCCFVLSPYYLFGFSTLSLLDSFRREIEGLSSYEPVITPLCSEISNGTICCDRTGLRSDICVMKGDVRTNSASSSIFLFTSSTNNNTKPEKIKPYTRKWETSVMDTVQELNLITKDSNKSSDRVCDVYHDVPAVFFSTGGYTGNVYHEFNDGIIPLFITSQHYNKKVVFVIVEYHDWWEMKYGDVVSQLSDYPLVDFNGDTRTHCFKEATVGLRIHDELTVNSSLVIGNQTIVDFRNVLDRGYSHRIQSLTQEETEANVTALDFKKKPKLVILSRNGSSRAILNENLLVELAEKTGFNVEVLRPQKTTEMAKIYRSLNTSDVMIGVHGAAMTHFLFLKPKTVFIQIIPLGTDWAAETYYGEPAKKLGLKYVGYKIAPKESSLYEEYGKDDPVIRDPDSLNDKGWEYTKKIYLQGQNVKLDLRRFRETLTRSYDFSIRRRFREDYLLHRED* Microarray data shows that thecoding sequence was expressed in the following experiments, which showsthat the promoter would be useful to modulate expression in situationssimilar to the following: CDNA_ID SHORT_NAME EXPT_REP_ID IS_UP 12735575At_42deg_Heat 20000171 − 12735575 At_42deg_Heat 20000173 − 12735575At_2mM_SA 20000181 + 12735575 At_2mM_SA 20000182 + 12735575 At_Shoots20000184 − 12735575 At_Roots 20000185 − 12735575 At_Siliques 20000234 −12735575 At_Siliques 20000235 − 12735575 At_Siliques 20000236 − 12735575At_Open_Flower 20000264 − 12735575 At_Open_Flower 20000265 − 12735575At_100mM_NaCl 20000268 − 12735575 At_Open_Flower 20000286 − 12735575At_Pollen 20000326 − 12735575 At_Shoots 20000438 − 12735575At_1uM_BR-BRZ 20000441 + 12735575 At_10percent_PEG 20000460 + 12735575At_Guard_Cells 20000495 − 12735575 At_10percent_PEG 20000527 + 12735575At_100uM_ABA_Mutants 20000573 − 12735575 At_100uM_ABA_Mutants 20000574 −12735575 At_Herbicide_Mutants 20000640 − 12735575 At_15mM_NH4NO3_L-to-H20000709 + 12735575 At_Line_Comparisons 20001192 − 12735575At_Line_Comparisons 20001195 − 12735575 At_Far-red-induction 20001247 +12735575 At_Far-red-induction 20001248 + 12735575 At_Line_Comparisons20001308 + 12735575 At_Interploidy_Crosses 20001316 − 12735575At_Line_Comparisons 20001319 − 12735575 At_Line_Comparisons 20001347 −12735575 At_Far-red-induction 20001450 + 12735575 At_Drought_Soil_Dry20001557 + 12735575 At_Interploidy_Crosses 20001653 + 12735575At_Interploidy_Crosses 20001654 + 12735575 At_Interploidy_Crosses20001703 − 12735575 At_Interploidy_Crosses 20001704 − 12735575At_50mM_NH4NO3_L-to-H 20001757 − 12735575 At_Interploidy_Crosses20001853 − 12735575 At_Drought_Reproduction 20001905 + 12735575At_Drought_Reproduction 20001911 + 12735575 At_Line_Comparisons20002007 + 12735575 At_Line_Comparisons 20002008 + 12735575At_Line_Comparisons 20002009 + 12735575 At_Line_Comparisons 20002010 +12735575 At_Line_Comparisons 20002012 + 12735575 At_8deg_Cold 20002103 −12735575 At_8deg_Cold 20002105 − 12735575 At_8deg_Cold 20002108 −12735575 At_8deg_Cold 20002109 − The parameters for the microarrayexperiments listed above by Expt_Rep_ID and Short_Name are as followbelow: CDNA_ID SHORT_NAME EXPT_REP_ID PARAM_NAME VALUE 12735575At_42deg_Heat 20000171 Timepoint (hr) 1 12735575 At_42deg_Heat 20000171Age (day) 14 12735575 At_42deg_Heat 20000171 Temperature (deg C.) 42 vs.22 12735575 At_42deg_Heat 20000171 Organism A. thaliana 12735575At_42deg_Heat 20000171 Tissue Aerial 12735575 At_42deg_Heat 20000171Plant Line WS 12735575 At_42deg_Heat 20000173 Timepoint (hr) 6 12735575At_42deg_Heat 20000173 Age (day) 14 12735575 At_42deg_Heat 20000173Temperature (deg C.) 42 vs. 22 12735575 At_42deg_Heat 20000173 OrganismA. thaliana 12735575 At_42deg_Heat 20000173 Tissue Aerial 12735575At_42deg_Heat 20000173 Plant Line WS 12735575 At_2mM_SA 20000181Timepoint (hr) 1 12735575 At_2mM_SA 20000181 Age (day) 14 12735575At_2mM_SA 20000181 Treatment 2 mM SA vs. No Treatment 12735575 At_2mM_SA20000181 Organism A. thaliana 12735575 At_2mM_SA 20000181 Tissue Aerial12735575 At_2mM_SA 20000181 Plant Line WS 12735575 At_2mM_SA 20000182Timepoint (hr) 6 12735575 At_2mM_SA 20000182 Age (day) 14 12735575At_2mM_SA 20000182 Treatment 2 mM SA vs. No Treatment 12735575 At_2mM_SA20000182 Organism A. thaliana 12735575 At_2mM_SA 20000182 Tissue Aerial12735575 At_2mM_SA 20000182 Plant Line WS 12735575 At_Shoots 20000184Age (day) 7 vs. 21 12735575 At_Shoots 20000184 Organism A. thaliana12735575 At_Shoots 20000184 Tissue Shoots vs. Whole Plant 12735575At_Shoots 20000184 Plant Line WS 12735575 At_Roots 20000185 Age (day) 7vs. 21 12735575 At_Roots 20000185 Organism A. thaliana 12735575 At_Roots20000185 Tissue Roots vs. Whole Plant 12735575 At_Roots 20000185 PlantLine WS 12735575 At_Siliques 20000234 Age (day) 21 12735575 At_Siliques20000234 Tissue <5 mm Siliques vs. Whole Plant 12735575 At_Siliques20000234 Organism A. thaliana 12735575 At_Siliques 20000234 Plant LineWS 12735575 At_Siliques 20000235 Age (day) 21 12735575 At_Siliques20000235 Tissue 5-10 mm Siliques vs. Whole Plant 12735575 At_Siliques20000235 Organism A. thaliana 12735575 At_Siliques 20000235 Plant LineWS 12735575 At_Siliques 20000236 Age (day) 21 12735575 At_Siliques20000236 Tissue >10 mm Siliques vs. Whole Plant 12735575 At_Siliques20000236 Organism A. thaliana 12735575 At_Siliques 20000236 Plant LineWS 12735575 At_Open_Flower 20000264 Age (day) 21 12735575 At_Open_Flower20000264 Organism A. thaliana 12735575 At_Open_Flower 20000264 TissueOpen Flower vs. Whole Plant 12735575 At_Open_Flower 20000264 Plant LineWS 12735575 At_Open_Flower 20000265 Age (day) 21 12735575 At_Open_Flower20000265 Organism A. thaliana 12735575 At_Open_Flower 20000265 TissueClosed Flower vs. Whole Plant 12735575 At_Open_Flower 20000265 PlantLine WS 12735575 At_100mM_NaCl 20000268 Timepoint (hr) 6 12735575At_100mM_NaCl 20000268 Age (day) 14 12735575 At_100mM_NaCl 20000268Treatment 100 mM NaCl vs. No Treatment 12735575 At_100mM_NaCl 20000268Organism A. thaliana 12735575 At_100mM_NaCl 20000268 Tissue Whole Plant12735575 At_100mM_NaCl 20000268 Plant Line WS 12735575 At_Open_Flower20000286 Age (day) 21 12735575 At_Open_Flower 20000286 Organism A.thaliana 12735575 At_Open_Flower 20000286 Tissue Half Open vs. WholePlant 12735575 At_Open_Flower 20000286 Plant Line WS 12735575 At_Pollen20000326 Age (day) 0 vs. 21 12735575 At_Pollen 20000326 Organism A.thaliana 12735575 At_Pollen 20000326 Tissue Pollen vs. Whole Plant12735575 At_Pollen 20000326 Plant Line WS 12735575 At_Shoots 20000438Age (day) 14 vs. 21 12735575 At_Shoots 20000438 Organism A. thaliana12735575 At_Shoots 20000438 Tissue Shoots vs. Whole Plant 12735575At_Shoots 20000438 Plant Line WS 12735575 At_1uM_BR-BRZ 20000441Treatment 1uM BR vs. No Treatment 12735575 At_1uM_BR-BRZ 20000441 TissueShoot Apices 12735575 At_10percent_PEG 20000460 Age (day) 12 12735575At_10percent_PEG 20000460 Timepoint (day) 12 12735575 At_10percent_PEG20000460 Treatment 10 percent PEG vs. No Treatment 12735575At_10percent_PEG 20000460 Organism A. thaliana 12735575 At_10percent_PEG20000460 Tissue Whole Plant 12735575 At_10percent_PEG 20000460 PlantLine WS 12735575 At_Guard_Cells 20000495 Harvest Date 08 Feb. 200212735575 At_Guard_Cells 20000495 Organism A. thaliana 12735575At_Guard_Cells 20000495 Tissue Guard Cells vs. Leaves 12735575At_10percent_PEG 20000527 Age (day) 20 12735575 At_10percent_PEG20000527 Timepoint (day) 20 12735575 At_10percent_PEG 20000527 Treatment10 percent PEG vs. No Treatment 12735575 At_10percent_PEG 20000527Organism A. thaliana 12735575 At_10percent_PEG 20000527 Tissue WholePlant 12735575 At_10percent_PEG 20000527 Plant Line WS 12735575At_100uM_ABA_Mutants 20000573 Organism A. thaliana 12735575At_100uM_ABA_Mutants 20000573 Plant Line CS22 vs. Ler wt 12735575At_100uM_ABA_Mutants 20000573 Timepoint (hr) N/A 12735575At_100uM_ABA_Mutants 20000573 Treatment None 12735575At_100uM_ABA_Mutants 20000573 Tissue Whole Plant 12735575At_100uM_ABA_Mutants 20000574 Organism A. thaliana 12735575At_100uM_ABA_Mutants 20000574 Plant Line CS23 vs. Ler wt 12735575At_100uM_ABA_Mutants 20000574 Timepoint (hr) N/A 12735575At_100uM_ABA_Mutants 20000574 Treatment None 12735575At_100uM_ABA_Mutants 20000574 Tissue Whole Plant 12735575At_Herbicide_Mutants 20000640 Timepoint (hr) 12 12735575At_Herbicide_Mutants 20000640 Plant Line 05377RR/BR27173 12735575At_Herbicide_Mutants 20000640 Treatment Roundup vs. No Treatment12735575 At_Herbicide_Mutants 20000640 Tissue Seedlings 12735575At_15mM_NH4NO3_L-to-H 20000709 Timepoint (hr) 4 12735575At_15mM_NH4NO3_L-to-H 20000709 Age (hr) 14 12735575At_15mM_NH4NO3_L-to-H 20000709 Treatment 15 mM NH4NO3 vs. 30 mM Mannitol12735575 At_15mM_NH4NO3_L-to-H 20000709 Organism A. thaliana 12735575At_15mM_NH4NO3_L-to-H 20000709 Tissue Aerial 12735575At_15mM_NH4NO3_L-to-H 20000709 Plant Line WS 12735575At_Line_Comparisons 20001192 Plant Line WBin4-WX13R-A vs. WS 12735575At_Line_Comparisons 20001195 Plant Line WBin4-WX14-B vs. WS 12735575At_Far-red-induction 20001247 Timepoint (hr) 1 12735575At_Far-red-induction 20001247 Age (day) 7 12735575 At_Far-red-induction20001247 Organism A. thaliana 12735575 At_Far-red-induction 20001247Plant Line Columbia 12735575 At_Far-red-induction 20001247 Light Far-redvs. White 12735575 At_Far-red-induction 20001247 Tissue Whole Plant12735575 At_Far-red-induction 20001248 Timepoint (hr) 4 12735575At_Far-red-induction 20001248 Age (day) 7 12735575 At_Far-red-induction20001248 Organism A. thaliana 12735575 At_Far-red-induction 20001248Plant Line Columbia 12735575 At_Far-red-induction 20001248 Light Far-redvs. White 12735575 At_Far-red-induction 20001248 Tissue Whole Plant12735575 At_Line_Comparisons 20001308 Plant Line WBin4-WX49-C vs. WS12735575 At_Interploidy_Crosses 20001316 Age (day) 5 12735575At_Interploidy_Crosses 20001316 Organism A. thaliana 12735575At_Interploidy_Crosses 20001316 Plant Line Columbia 12735575At_Interploidy_Crosses 20001316 Cross hemi × 2X vs. 2X × 2X 12735575At_Interploidy_Crosses 20001316 Tissue Siliques 12735575At_Line_Comparisons 20001319 Plant Line WBin4-WX24-A vs. WS 12735575At_Line_Comparisons 20001347 Plant Line ME01604-01 vs. WS 12735575At_Far-red-induction 20001450 Age (day) 7 12735575 At_Far-red-induction20001450 Timepoint (hr) 8 12735575 At_Far-red-induction 20001450Organism A. thaliana 12735575 At_Far-red-induction 20001450 Plant LineColumbia 12735575 At_Far-red-induction 20001450 Light Far-red vs. White12735575 At_Far-red-induction 20001450 Tissue Whole Plant 12735575At_Drought_Soil_Dry 20001557 Post Timepoint (hr) 3 12735575At_Drought_Soil_Dry 20001557 Timepoint (day) 13 12735575At_Drought_Soil_Dry 20001557 Age (day) 27 12735575 At_Drought_Soil_Dry20001557 Organism A. thaliana 12735575 At_Drought_Soil_Dry 20001557Treatment Drought vs. No Drought 12735575 At_Drought_Soil_Dry 20001557Post-Treatment Re-Water vs. No Drought 12735575 At_Drought_Soil_Dry20001557 Plant Line WS 12735575 At_Interploidy_Crosses 20001653 Age(day) 5 12735575 At_Interploidy_Crosses 20001653 Cross 2X × 6X vs. 2X× 2X 12735575 At_Interploidy_Crosses 20001653 Organism A. thaliana12735575 At_Interploidy_Crosses 20001653 Plant Line Columbia 12735575At_Interploidy_Crosses 20001653 Tissue Siliques 12735575At_Interploidy_Crosses 20001654 Age (day) 5 12735575At_Interploidy_Crosses 20001654 Cross 6X × 2X vs. 2X × 2X 12735575At_Interploidy_Crosses 20001654 Organism A. thaliana 12735575At_Interploidy_Crosses 20001654 Plant Line Columbia 12735575At_Interploidy_Crosses 20001654 Tissue Siliques 12735575At_Interploidy_Crosses 20001703 Age (day) 5 12735575At_Interploidy_Crosses 20001703 Cross 2X × 4X vs. 2X × 2X 12735575At_Interploidy_Crosses 20001703 Organism A. thaliana 12735575At_Interploidy_Crosses 20001703 Plant Line Columbia 12735575At_Interploidy_Crosses 20001703 Tissue Siliques 12735575At_Interploidy_Crosses 20001704 Age (day) 5 12735575At_Interploidy_Crosses 20001704 Cross 4X × 2X vs. 2X × 2X 12735575At_Interploidy_Crosses 20001704 Organism A. thaliana 12735575At_Interploidy_Crosses 20001704 Plant Line Columbia 12735575At_Interploidy_Crosses 20001704 Tissue Siliques 12735575At_50mM_NH4NO3_L-to-H 20001757 Timepoint (hr) 6 12735575At_50mM_NH4NO3_L-to-H 20001757 Treatment 50 mM NH4NO3 vs 100 mM Mannitol12735575 At_50mM_NH4NO3_L-to-H 20001757 Tissue Leaf 12735575At_Interploidy_Crosses 20001853 Age (day) 5 12735575At_Interploidy_Crosses 20001853 Organism A. thaliana 12735575At_Interploidy_Crosses 20001853 Plant Line Columbia 12735575At_Interploidy_Crosses 20001853 Cross Fis1 vs. 2X × 2X 12735575At_Interploidy_Crosses 20001853 Tissue Siliques 12735575At_Drought_Reproduction 20001905 Timepoint (day) 10 12735575At_Drought_Reproduction 20001905 Age (day) 40 12735575At_Drought_Reproduction 20001905 Organism A. thaliana 12735575At_Drought_Reproduction 20001905 Treatment Drought vs. No Drought12735575 At_Drought_Reproduction 20001905 Tissue Rosettes 12735575At_Drought_Reproduction 20001905 Plant Line WS 12735575At_Drought_Reproduction 20001911 Timepoint (day) 10 12735575At_Drought_Reproduction 20001911 Age (day) 40 12735575At_Drought_Reproduction 20001911 Organism A. thaliana 12735575At_Drought_Reproduction 20001911 Treatment Drought vs. No Drought12735575 At_Drought_Reproduction 20001911 Tissue Flowers 12735575At_Drought_Reproduction 20001911 Plant Line WS 12735575At_Line_Comparisons 20002007 Plant Line ME03793 vs. WS 12735575At_Line_Comparisons 20002008 Plant Line ME03766 vs. WS 12735575At_Line_Comparisons 20002009 Plant Line ME01642 vs. WS 12735575At_Line_Comparisons 20002010 Plant Line ME02031 vs. WS 12735575At_Line_Comparisons 20002012 Plant Line SALK_073455 vs. Columbia12735575 At_8deg_Cold 20002103 Timepoint (hr) 2 12735575 At_8deg_Cold20002103 Age (day) 7 12735575 At_8deg_Cold 20002103 Temperature (deg C.)8 vs. 22 12735575 At_8deg_Cold 20002103 Organism A. thaliana 12735575At_8deg_Cold 20002103 Tissue Whole Plant 12735575 At_8deg_Cold 20002103Plant Line WS 12735575 At_8deg_Cold 20002105 Age (day) 7 12735575At_8deg_Cold 20002105 Timepoint (hr) 8 12735575 At_8deg_Cold 20002105Temperature (deg C.) 8 vs. 22 12735575 At_8deg_Cold 20002105 Organism A.thaliana 12735575 At_8deg_Cold 20002105 Tissue Whole Plant 12735575At_8deg_Cold 20002105 Plant Line WS 12735575 At_8deg_Cold 20002108 Age(day) 14 12735575 At_8deg_Cold 20002108 Timepoint (hr) 168 12735575At_8deg_Cold 20002108 Temperature (deg C.) 8 vs. 22 12735575At_8deg_Cold 20002108 Organism A. thaliana 12735575 At_8deg_Cold20002108 Tissue Whole Plant 12735575 At_8deg_Cold 20002108 Plant Line WS12735575 At_8deg_Cold 20002109 Age (day) 16 12735575 At_8deg_Cold20002109 Timepoint (hr) 216 12735575 At_8deg_Cold 20002109 Temperature(deg C.) 8 vs. 22 12735575 At_8deg_Cold 20002109 Organism A. thaliana12735575 At_8deg_Cold 20002109 Tissue Whole Plant 12735575 At_8deg_Cold20002109 Plant Line WS Promoter YP0381 Modulates the gene: Unknownexpressed protein The GenBank description of the gene: NM_113878Arabidopsis thaliana expressed protein (At3g29575) mRNA, complete cdsgi|30689672|ref|NM_113878.3|[30689672] The promoter sequence:5′tcattacattgaaaaagaaaattaattgtctttactcatgtttattctatacaaataaaaatattaaccaaccatcgcactaacaaaatagaaatcttattctaatcacttaattgttgacaattaaatcattgaaaaatacacttaaatgtcaaatattcgttttgcatacttttcaatttaaatacatttaaagttcgacaagttgcgtttactatcatagaaaactaaatctcctaccaaagcgaaatgaaactactaaagcgacaggcaggttacataacctaacaaatctccacgtgtcaattaccaagagaaaaaaagagaagataagcggaacacgtggtagcacaaaaaagataatgtgatttaaattaaaaaacaaaaacaaagacacgtgacgacctgacgctgcaacatcccaccttacaacgtaataaccactgaacataagacacgtgtacgatcttgtctttgttttctcgatgaaaaccacgtgggtgctcaaagtccttgggtcagagtcttccatgattccacgtgtcgttaatgcaccaaacaagggtactttcggtattttggcttccgcaaattagacaaaacagctttttgtttgattgatttttctcttctctttttccatctaaattctctttgggctcttaatttctttttgagtgttcgttcgagatttgtcggagattttttcggtaaatgttgaaattttgtgggatttttttttatttctttattaaacttttttttattgaattTATAaaaagggaaggtcgtcattaatcgaagaaatggaatcttccaaaatttgatattttgctgttttcttgggatttgaattgctctttatcatcaagaatctgttaaaatttctaatctaaaatctaagttgagaaaaagagagatctctaatttaaccggaattaatattctcc3′-cATG The promoter was cloned from the organism: Arabidopsis thaliana,Columbia ecotype Alternative nucleotides: Predicted (Columbia)Experimental (Columbia) Predicted Position (bp) MismatchPredicted/Experimental 966 Sequence read error —/a The promoter wascloned in the vector: pNewbin4-HAP1-GFP When cloned into the vector thepromoter was operably linked to a marker, which was the type: GFP-ERPromoter-marker vector was tested in: Arabidopsis thaliana, Columbiaecotype Generation screened: XT1 Mature XT2 Seedling T2 Mature T3Seedling The spatial expression of the promoter-marker vector was foundobserved in and would be useful in expression in any or all of thefollowing: Flower L pedicel H nectary L epidermis Hypocotyl L vascularPrimary Root H vascular Observed expression pattern: T1 mature: Highexpression in nectary glands of flowers. Low expression in epidermis ofpedicles developing flowers. T2 seedling: GFP expressed in root andhypocotyl vasculature. Misc. promoter information: Bidirectionality:Pass Exons: Pass   Repeats: No Optional Promoter Fragments: 5′ UTRregion at base pairs 671-975. The Ceres cDNA ID of the endogenous codingsequence to the promoter: 12736859 cDNA nucleotide sequence:AAATTCTCTTTGGGCTCTTAATTTCTTTTTGAGTGTTCGTTCGAGATTTGTCGGAGATTTTTTCGGTAAATGTTGAAATTTTGTGGGATTTTTTTTTATTTCTTTATTAAACTTTTTTTTATTGAATTTATAAAAAGGGAAGGTCGTCATTAATCGAAGAAATGGAATCTTCCAAAATTTGATATTTTGCTGTTTTCTTGGGATTTGAATTGCTCTTTATCATCAAGAATCTGTTAAAATTTCTAATCTAAAATCTAAGTTGAGAAAAAGAGAGATCTCTAATTTAACCGGAATTAATATTCTCCGACCGAAGTTATTATGTTGCAGGCTCATGTCGAAGAAACAGAGATTGTCTGAAGAAGATGGAGAGGTAGAGATTGAGTTAGACTTAGGTCTATCTCTAAATGGAAGATTTGGTGTTGACCCACTTGCGAAAACAAGGCTTATGAGGTCTACGTCGGTTCTTGATTTGGTGGTCAACGATAGGTCAGGGCTGAGTAGGACTTGTTCGTTACCCGTGGAGACGGAGGAAGAGTGGAGGAAGAGGAAGGAGTTGCAGAGTTTGAGGAGGCTTGAGGCTAAGAGAAAGAGATCAGAGAAGCAGAGGAAACATAAAGCTTGTGGTGGTGAAGAGAAGGTTGTGGAAGAAGGATCTATTGGTTCTTCTGGTAGTGGTTCCTCTGGTTTGTCTGAAGTTGATACTCTTCTTCCTCCTGTTCAAGCAACAACGAACAAGTCCGTGGAAACAAGCCCTTCAAGTGCCCAATCTCAGCCCGAGAATTTGGGCAAAGAAGCGAGCCAAAACATTATAGAGGACATGCCATTCGTGTCAACAACAGGCGATGGACCGAACGGGAAAAAGATTAATGGGTTTCTGTATCGGTACCGCAAAGGTGAGGAGGTGAGGATTGTCTGTGTGTGTCATGGAAGCTTCCTCTCACCGGCAGAATTCGTTAAGCATGCTGGTGGTGGTGACGTTGCACATCCCTTAAAGCACATCGTTGTAAATCCATCTCCCTTCTTGTGACCCTTTGGGTCTCTTTTGAGGGGTTTGTTGTATCGGAACCATGTTACAAATCCTCATTATCTCCGAGGTGTATAAACATAAATTTATCGAACTCGCAATTTTCAGATTTTGTACTTAAAAGAATGGTTTCATTCGTTGAGATTAATTTTAGACCTTTTTCTTGTAC Codingsequence:MSKKQRLSEEDGEVEIELDLGLSLNGRFGVDPLAKTRLMRSTSVLDLVVNDRSGLSRTCSLPVETEEEWRKRKELQSLRRLEAKRKRSEKQRKHKACGGEEKVVEEGSIGSSGSGSSGLSEVDTLLPPVQATTNKSVETSPSSAQSQPENLGKEASQNIIEDMPFVSTTGDGPNGKKINGFLYRYRKGEEVRIVCVCHGSFLSPAEFVKHAGGGDVAHPLKHIVVNPSPFL* Microarray data shows that the codingsequence was expressed in the following experiments, which shows thatthe promoter would be useful to modulate expression in situationssimilar to the following: CDNA_ID SHORT_NAME EXPT_REP_ID IS_UP 12736859At_100uM_ABA 20000166 + 12736859 At_100uM_ABA 20000169 + 12736859At_Germinating_Seeds 20000179 + 12736859 At_Germinating_Seeds 20000180 +12736859 At_2mM_SA 20000182 + 12736859 At_Root-Tips-vs-Tops 20000227 +12736859 At_Siliques 20000234 − 12736859 At_Siliques 20000236 − 12736859At_Open_Flower 20000264 − 12736859 At_Open_Flower 20000265 − 12736859At_Drought 20000267 + 12736859 At_100mM_NaCl 20000268 + 12736859At_Open_Flower 20000286 − 12736859 At_Drought 20000436 + 12736859At_Drought 20000437 + 12736859 At_CS6879_Shoots-Roots 20000451 +12736859 At_100uM_ABA 20000453 + 12736859 At_100uM_ABA 20000455 +12736859 At_42deg_Heat 20000458 + 12736859 At_10percent_PEG 20000460 +12736859 At_100uM_ABA_Mutants 20000574 − 12736859 At_CS8548_Mutant20000606 − 12736859 At_Herbicide_Mutants 20000639 + 12736859At_15mM_NH4NO3_L-to-H 20000709 − 12736859 At_Petals 20000794 − 12736859At_Line_Comparisons 20001151 + 12736859 At_Line_Comparisons 20001184 +12736859 At_Far-red-induction 20001247 + 12736859 At_Far-red-induction20001248 + 12736859 At_Line_Comparisons 20001307 + 12736859At_Line_Comparisons 20001309 − 12736859 At_Line_Comparisons 20001310 −12736859 At_Line_Comparisons 20001347 + 12736859 At_Far-red-induction20001450 + 12736859 At_Far-red-induction 20001451 + 12736859At_Far-red-enriched 20001504 + 12736859 At_Drought_Soil_Dry 20001553 +12736859 At_Drought_Soil_Dry 20001554 + 12736859 At_Drought_Soil_Dry20001556 + 12736859 At_Drought_Soil_Dry 20001559 + 12736859At_Interploidy_Crosses 20001654 + 12736859 At_Far-red-enriched-adult20001768 + 12736859 At_Far-red-enriched-adult 20001769 + 12736859At_Far-red-enriched-adult 20001770 + 12736859 At_Far-red-enriched-adult20001773 + 12736859 At_Far-red-enriched-adult 20001774 + 12736859At_Drought_Reproduction 20001904 + 12736859 At_Drought_Reproduction20001906 + 12736859 At_Drought_Reproduction 20001908 + 12736859At_Drought_Reproduction 20001910 + 12736859 At_8deg_Cold 20002105 +12736859 At_8deg_Cold 20002108 − 12736859 At_Drought-Air-Dry 20002254 +12736859 At_Drought-Air-Dry 20002256 + The parameters for the microarrayexperiments listed above by Expt_Rep_ID and Short_Name are as followbelow: CDNA_ID SHORT_NAME EXPT_REP_ID PARAM_NAME VALUE 12736859At_100uM_ABA 20000166 Timepoint (hr) 1 12736859 At_100uM_ABA 20000166Age (day) 14 12736859 At_100uM_ABA 20000166 Treatment 100 uM ABA vs. NoTreatment 12736859 At_100uM_ABA 20000166 Organism A. thaliana 12736859At_100uM_ABA 20000166 Tissue Aerial 12736859 At_100uM_ABA 20000166 PlantLine WS 12736859 At_100uM_ABA 20000169 Timepoint (hr) 6 12736859At_100uM_ABA 20000169 Age (day) 14 12736859 At_100uM_ABA 20000169Treatment 100 uM ABA vs. No Treatment 12736859 At_100uM_ABA 20000169Organism A. thaliana 12736859 At_100uM_ABA 20000169 Tissue Aerial12736859 At_100uM_ABA 20000169 Plant Line WS 12736859At_Germinating_Seeds 20000179 Age (hr) 6 vs. 0 12736859At_Germinating_Seeds 20000179 Organism A. thaliana 12736859At_Germinating_Seeds 20000179 Tissue Germinating Seeds 12736859At_Germinating_Seeds 20000179 Plant Line WS 12736859At_Germinating_Seeds 20000180 Age (hr) 24 vs. 0 12736859At_Germinating_Seeds 20000180 Organism A. thaliana 12736859At_Germinating_Seeds 20000180 Tissue Germinating Seeds 12736859At_Germinating_Seeds 20000180 Plant Line WS 12736859 At_2mM_SA 20000182Timepoint (hr) 6 12736859 At_2mM_SA 20000182 Age (day) 14 12736859At_2mM_SA 20000182 Treatment 2 mM SA vs. No Treatment 12736859 At_2mM_SA20000182 Organism A. thaliana 12736859 At_2mM_SA 20000182 Tissue Aerial12736859 At_2mM_SA 20000182 Plant Line WS 12736859 At_Root-Tips-vs-Tops20000227 Age (day) 7, 10, 14 12736859 At_Root-Tips-vs-Tops 20000227Organism A. thaliana 12736859 At_Root-Tips-vs-Tops 20000227 Tissue RootTips vs. Root Tops 12736859 At_Root-Tips-vs-Tops 20000227 Plant Line WS12736859 At_Siliques 20000234 Age (day) 21 12736859 At_Siliques 20000234Tissue <5 mm Siliques vs. Whole Plant 12736859 At_Siliques 20000234Organism A. thaliana 12736859 At_Siliques 20000234 Plant Line WS12736859 At_Siliques 20000236 Age (day) 21 12736859 At_Siliques 20000236Tissue >10 mm Siliques vs. Whole Plant 12736859 At_Siliques 20000236Organism A. thaliana 12736859 At_Siliques 20000236 Plant Line WS12736859 At_Open_Flower 20000264 Age (day) 21 12736859 At_Open_Flower20000264 Organism A. thaliana 12736859 At_Open_Flower 20000264 TissueOpen Flower vs. Whole Plant 12736859 At_Open_Flower 20000264 Plant LineWS 12736859 At_Open_Flower 20000265 Age (day) 21 12736859 At_Open_Flower20000265 Organism A. thaliana 12736859 At_Open_Flower 20000265 TissueClosed Flower vs. Whole Plant 12736859 At_Open_Flower 20000265 PlantLine WS 12736859 At_Drought 20000267 Timepoint (hr) 6 12736859At_Drought 20000267 Age (day) 7 12736859 At_Drought 20000267 Organism A.thaliana 12736859 At_Drought 20000267 Treatment Drought vs. No Drought12736859 At_Drought 20000267 Tissue Whole Plant 12736859 At_Drought20000267 Plant Line WS 12736859 At_100mM_NaCl 20000268 Timepoint (hr) 612736859 At_100mM_NaCl 20000268 Age (day) 14 12736859 At_100mM_NaCl20000268 Treatment 100 mM NaCl vs. No Treatment 12736859 At_100mM_NaCl20000268 Organism A. thaliana 12736859 At_100mM_NaCl 20000268 TissueWhole Plant 12736859 At_100mM_NaCl 20000268 Plant Line WS 12736859At_Open_Flower 20000286 Age (day) 21 12736859 At_Open_Flower 20000286Organism A. thaliana 12736859 At_Open_Flower 20000286 Tissue Half Openvs. Whole Plant 12736859 At_Open_Flower 20000286 Plant Line WS 12736859At_Drought 20000436 Age (day) 7 12736859 At_Drought 20000436 Timepoint(hr) 12 12736859 At_Drought 20000436 Organism A. thaliana 12736859At_Drought 20000436 Treatment Drought vs. No Drought 12736859 At_Drought20000436 Tissue Whole Plant 12736859 At_Drought 20000436 Plant Line WS12736859 At_Drought 20000437 Age (day) 8 12736859 At_Drought 20000437Timepoint (hr) 24 12736859 At_Drought 20000437 Organism A. thaliana12736859 At_Drought 20000437 Treatment Drought vs. No Drought 12736859At_Drought 20000437 Tissue Whole Plant 12736859 At_Drought 20000437Plant Line WS 12736859 At_CS6879_Shoots-Roots 20000451 Age (day) 1412736859 At_CS6879_Shoots-Roots 20000451 Organism A. thaliana 12736859At_CS6879_Shoots-Roots 20000451 Plant Line CS6879 vs. WS 12736859At_CS6879_Shoots-Roots 20000451 Tissue Roots 12736859 At_100uM_ABA20000453 Age (day) 15 12736859 At_100uM_ABA 20000453 Timepoint (hr) 2412736859 At_100uM_ABA 20000453 Treatment 100 uM ABA vs. No Treatment12736859 At_100uM_ABA 20000453 Organism A. thaliana 12736859At_100uM_ABA 20000453 Tissue Aerial 12736859 At_100uM_ABA 20000453 PlantLine WS 12736859 At_100uM_ABA 20000455 Age (day) 16 12736859At_100uM_ABA 20000455 Timepoint (hr) 48 12736859 At_100uM_ABA 20000455Treatment 100 uM ABA vs. No Treatment 12736859 At_100uM_ABA 20000455Organism A. thaliana 12736859 At_100uM_ABA 20000455 Tissue Aerial12736859 At_100uM_ABA 20000455 Plant Line WS 12736859 At_42deg_Heat20000458 Timepoint (hr) 8 12736859 At_42deg_Heat 20000458 Age (day) 1412736859 At_42deg_Heat 20000458 Temperature (deg C.) 42 vs. 22 12736859At_42deg_Heat 20000458 Organism A. thaliana 12736859 At_42deg_Heat20000458 Tissue Aerial 12736859 At_42deg_Heat 20000458 Plant Line WS12736859 At_10percent_PEG 20000460 Age (day) 12 12736859At_10percent_PEG 20000460 Timepoint (day) 12 12736859 At_10percent_PEG20000460 Treatment 10 percent PEG vs. No Treatment 12736859At_10percent_PEG 20000460 Organism A. thaliana 12736859 At_10percent_PEG20000460 Tissue Whole Plant 12736859 At_10percent_PEG 20000460 PlantLine WS 12736859 At_100uM_ABA_Mutants 20000574 Organism A. thaliana12736859 At_100uM_ABA_Mutants 20000574 Plant Line CS23 vs. Ler wt12736859 At_100uM_ABA_Mutants 20000574 Timepoint (hr) N/A 12736859At_100uM_ABA_Mutants 20000574 Treatment None 12736859At_100uM_ABA_Mutants 20000574 Tissue Whole Plant 12736859At_CS8548_Mutant 20000606 Age (day) 14 12736859 At_CS8548_Mutant20000606 Plant Line CS8548 vs. wt 12736859 At_CS8548_Mutant 20000606Tissue Whole Plant 12736859 At_Herbicide_Mutants 20000639 Timepoint (hr)4 12736859 At_Herbicide_Mutants 20000639 Plant Line 05377RR/BR2717312736859 At_Herbicide_Mutants 20000639 Treatment Roundup vs. NoTreatment 12736859 At_Herbicide_Mutants 20000639 Tissue Seedlings12736859 At_15mM_NH4NO3_L-to-H 20000709 Timepoint (hr) 4 12736859At_15mM_NH4NO3_L-to-H 20000709 Age (hr) 14 12736859At_15mM_NH4NO3_L-to-H 20000709 Treatment 15 mM NH4NO3 vs. 30 mM Mannitol12736859 At_15mM_NH4NO3_L-to-H 20000709 Organism A. thaliana 12736859At_15mM_NH4NO3_L-to-H 20000709 Tissue Aerial 12736859At_15mM_NH4NO3_L-to-H 20000709 Plant Line WS 12736859 At_Petals 20000794Age (day) 23-25 days 12736859 At_Petals 20000794 Organism A. thaliana12736859 At_Petals 20000794 Tissue Petals vs. Whole plant 12736859At_Petals 20000794 Plant Line WS 12736859 At_Line_Comparisons 20001151Plant Line ME01339-01 vs. WS 12736859 At_Line_Comparisons 20001184 PlantLine ME01848-01 vs. WS 12736859 At_Far-red-induction 20001247 Timepoint(hr) 1 12736859 At_Far-red-induction 20001247 Age (day) 7 12736859At_Far-red-induction 20001247 Organism A. thaliana 12736859At_Far-red-induction 20001247 Plant Line Columbia 12736859At_Far-red-induction 20001247 Light Far-red vs. White 12736859At_Far-red-induction 20001247 Tissue Whole Plant 12736859At_Far-red-induction 20001248 Timepoint (hr) 4 12736859At_Far-red-induction 20001248 Age (day) 7 12736859 At_Far-red-induction20001248 Organism A. thaliana 12736859 At_Far-red-induction 20001248Plant Line Columbia 12736859 At_Far-red-induction 20001248 Light Far-redvs. White 12736859 At_Far-red-induction 20001248 Tissue Whole Plant12736859 At_Line_Comparisons 20001307 Plant Line WBin4-WX2-A vs. WS12736859 At_Line_Comparisons 20001309 Plant Line WBin4-WX49R-A vs. WS12736859 At_Line_Comparisons 20001310 Plant Line WBin4-WX17-A vs. WS12736859 At_Line_Comparisons 20001347 Plant Line ME01604-01 vs. WS12736859 At_Far-red-induction 20001450 Age (day) 7 12736859At_Far-red-induction 20001450 Timepoint (hr) 8 12736859At_Far-red-induction 20001450 Organism A. thaliana 12736859At_Far-red-induction 20001450 Plant Line Columbia 12736859At_Far-red-induction 20001450 Light Far-red vs. White 12736859At_Far-red-induction 20001450 Tissue Whole Plant 12736859At_Far-red-induction 20001451 Age (day) 8 12736859 At_Far-red-induction20001451 Timepoint (hr) 24 12736859 At_Far-red-induction 20001451Organism A. thaliana 12736859 At_Far-red-induction 20001451 Plant LineColumbia 12736859 At_Far-red-induction 20001451 Light Far-red vs. White12736859 At_Far-red-induction 20001451 Tissue Whole Plant 12736859At_Far-red-enriched 20001504 Timepoint (day) 6 12736859At_Far-red-enriched 20001504 Age (day) 10 12736859 At_Far-red-enriched20001504 Organism A. thaliana 12736859 At_Far-red-enriched 20001504Plant Line Columbia 12736859 At_Far-red-enriched 20001504 Light Far-redenriched vs. White 12736859 At_Far-red-enriched 20001504 Tissue WholePlant 12736859 At_Drought_Soil_Dry 20001553 Timepoint (day) 5 12736859At_Drought_Soil_Dry 20001553 Age (day) 19 12736859 At_Drought_Soil_Dry20001553 Organism A. thaliana 12736859 At_Drought_Soil_Dry 20001553Treatment Drought vs. No Drought 12736859 At_Drought_Soil_Dry 20001553Post Timepoint (hr) None 12736859 At_Drought_Soil_Dry 20001553Post-Treatment None 12736859 At_Drought_Soil_Dry 20001553 Plant Line WS12736859 At_Drought_Soil_Dry 20001554 Timepoint (day) 7 12736859At_Drought_Soil_Dry 20001554 Age (day) 21 12736859 At_Drought_Soil_Dry20001554 Organism A. thaliana 12736859 At_Drought_Soil_Dry 20001554Treatment Drought vs. No Drought 12736859 At_Drought_Soil_Dry 20001554Post Timepoint (hr) None 12736859 At_Drought_Soil_Dry 20001554Post-Treatment None 12736859 At_Drought_Soil_Dry 20001554 Plant Line WS12736859 At_Drought_Soil_Dry 20001556 Timepoint (day) 12 12736859At_Drought_Soil_Dry 20001556 Age (day) 26 12736859 At_Drought_Soil_Dry20001556 Organism A. thaliana 12736859 At_Drought_Soil_Dry 20001556Treatment Drought vs. No Drought 12736859 At_Drought_Soil_Dry 20001556Post Timepoint (hr) None 12736859 At_Drought_Soil_Dry 20001556Post-Treatment None 12736859 At_Drought_Soil_Dry 20001556 Plant Line WS12736859 At_Drought_Soil_Dry 20001559 Timepoint (day) 14 12736859At_Drought_Soil_Dry 20001559 Age (day) 28 12736859 At_Drought_Soil_Dry20001559 Post Timepoint (hr) 29 12736859 At_Drought_Soil_Dry 20001559Organism A. thaliana 12736859 At_Drought_Soil_Dry 20001559 TreatmentDrought vs. No Drought 12736859 At_Drought_Soil_Dry 20001559Post-Treatment Re-Water vs. No Drought 12736859 At_Drought_Soil_Dry20001559 Plant Line WS 12736859 At_Interploidy_Crosses 20001654 Age(day) 5 12736859 At_Interploidy_Crosses 20001654 Cross 6X × 2X vs. 2X× 2X 12736859 At_Interploidy_Crosses 20001654 Organism A. thaliana12736859 At_Interploidy_Crosses 20001654 Plant Line Columbia 12736859At_Interploidy_Crosses 20001654 Tissue Siliques 12736859At_Far-red-enriched-adult 20001768 Timepoint (hr) 1 12736859At_Far-red-enriched-adult 20001768 Age (day) 28 12736859At_Far-red-enriched-adult 20001768 Organism A. thaliana 12736859At_Far-red-enriched-adult 20001768 Tissue Aerial 12736859At_Far-red-enriched-adult 20001768 Plant Line Columbia 12736859At_Far-red-enriched-adult 20001768 Light Far-red enriched vs. White12736859 At_Far-red-enriched-adult 20001769 Timepoint (hr) 4 12736859At_Far-red-enriched-adult 20001769 Age (day) 28 12736859At_Far-red-enriched-adult 20001769 Organism A. thaliana 12736859At_Far-red-enriched-adult 20001769 Tissue Aerial 12736859At_Far-red-enriched-adult 20001769 Plant Line Columbia 12736859At_Far-red-enriched-adult 20001769 Light Far-red enriched vs. White12736859 At_Far-red-enriched-adult 20001770 Timepoint (hr) 8 12736859At_Far-red-enriched-adult 20001770 Age (day) 28 12736859At_Far-red-enriched-adult 20001770 Organism A. thaliana 12736859At_Far-red-enriched-adult 20001770 Tissue Aerial 12736859At_Far-red-enriched-adult 20001770 Plant Line Columbia 12736859At_Far-red-enriched-adult 20001770 Light Far-red enriched vs. White12736859 At_Far-red-enriched-adult 20001773 Age (day) 30 12736859At_Far-red-enriched-adult 20001773 Timepoint (hr) 48 12736859At_Far-red-enriched-adult 20001773 Organism A. thaliana 12736859At_Far-red-enriched-adult 20001773 Tissue Aerial 12736859At_Far-red-enriched-adult 20001773 Plant Line Columbia 12736859At_Far-red-enriched-adult 20001773 Light Far-red enriched vs. White12736859 At_Far-red-enriched-adult 20001774 Age (day) 31 12736859At_Far-red-enriched-adult 20001774 Timepoint (hr) 72 12736859At_Far-red-enriched-adult 20001774 Organism A. thaliana 12736859At_Far-red-enriched-adult 20001774 Tissue Aerial 12736859At_Far-red-enriched-adult 20001774 Plant Line Columbia 12736859At_Far-red-enriched-adult 20001774 Light Far-red enriched vs. White12736859 At_Drought_Reproduction 20001904 Timepoint (day) 7 12736859At_Drought_Reproduction 20001904 Age (day) 37 12736859At_Drought_Reproduction 20001904 Organism A. thaliana 12736859At_Drought_Reproduction 20001904 Treatment Drought vs. No Drought12736859 At_Drought_Reproduction 20001904 Tissue Rosettes 12736859At_Drought_Reproduction 20001904 Plant Line WS 12736859At_Drought_Reproduction 20001906 Timepoint (day) 5 12736859At_Drought_Reproduction 20001906 Age (day) 35 12736859At_Drought_Reproduction 20001906 Organism A. thaliana 12736859At_Drought_Reproduction 20001906 Treatment Drought vs. No Drought12736859 At_Drought_Reproduction 20001906 Tissue Siliques 12736859At_Drought_Reproduction 20001906 Plant Line WS 12736859At_Drought_Reproduction 20001908 Timepoint (day) 10 12736859At_Drought_Reproduction 20001908 Age (day) 40 12736859At_Drought_Reproduction 20001908 Organism A. thaliana 12736859At_Drought_Reproduction 20001908 Treatment Drought vs. No Drought12736859 At_Drought_Reproduction 20001908 Tissue Siliques 12736859At_Drought_Reproduction 20001908 Plant Line WS 12736859At_Drought_Reproduction 20001910 Timepoint (day) 7 12736859At_Drought_Reproduction 20001910 Age (day) 37 12736859At_Drought_Reproduction 20001910 Organism A. thaliana 12736859At_Drought_Reproduction 20001910 Treatment Drought vs. No Drought12736859 At_Drought_Reproduction 20001910 Tissue Flowers 12736859At_Drought_Reproduction 20001910 Plant Line WS 12736859 At_8deg_Cold20002105 Age (day) 7 12736859 At_8deg_Cold 20002105 Timepoint (hr) 812736859 At_8deg_Cold 20002105 Temperature (deg C.) 8 vs. 22 12736859At_8deg_Cold 20002105 Organism A. thaliana 12736859 At_8deg_Cold20002105 Tissue Whole Plant 12736859 At_8deg_Cold 20002105 Plant Line WS12736859 At_8deg_Cold 20002108 Age (day) 14 12736859 At_8deg_Cold20002108 Timepoint (hr) 168 12736859 At_8deg_Cold 20002108 Temperature(deg C.) 8 vs. 22 12736859 At_8deg_Cold 20002108 Organism A. thaliana12736859 At_8deg_Cold 20002108 Tissue Whole Plant 12736859 At_8deg_Cold20002108 Plant Line WS 12736859 At_Drought-Air-Dry 20002254 Timepoint(hr) 4 12736859 At_Drought-Air-Dry 20002254 Age (day) 35 12736859At_Drought-Air-Dry 20002254 Organism A. thaliana 12736859At_Drought-Air-Dry 20002254 Treatment Drought vs. No Drought 12736859At_Drought-Air-Dry 20002254 Tissue Roots 12736859 At_Drought-Air-Dry20002254 Plant Line WS 12736859 At_Drought-Air-Dry 20002256 Timepoint(hr) 4 12736859 At_Drought-Air-Dry 20002256 Age (day) 35 12736859At_Drought-Air-Dry 20002256 Organism A. thaliana 12736859At_Drought-Air-Dry 20002256 Treatment Drought vs. No Drought 12736859At_Drought-Air-Dry 20002256 Tissue Shoots 12736859 At_Drought-Air-Dry20002256 Plant Line WS Promoter YP0380 Modulates the gene: Responsive toDehydration 20 The GenBank description of the gene:: NM_128898Arabidopsis thaliana RD20 protein (At2g33380) mRNA, complete cdsgi|30685670|ref|NM_128898.2|[30685670] The promoter sequence:5′tttcaatgtatacaatcatcatgtgataaaaaaaaaaatgtaaccaatcaacacactgagatacggccaaaaaatggtaatacataaatgtttgtaggttttgtaatttaaatactttagttaagttatgattttattatttttgcttatcacttatacgaaatcatcaatctattggtatctcttaatcccgctttttaatttccaccgcacacgcaaatcagcaaatggttccagccacgtgcatgtgaccacatattgtggtcacagtactcgtcctttttttttcttttgtaatcaataaatttcaatcctaaaacttcacacattgagcacgtcggcaacgttagctcctaaatcataacgagcaaaaaagttcaaattagggtatatgatcaattgatcatcactacatgtctacataattaatatgtattcaaccggtcggtttgttgatactcatagttaagtatatatgtgctaattagaattaggatgaatcagttcttgcaaacaactacggtttcatataatatgggagtgttatgtacaaaatgaaagaggatggatcattctgagatgttatgggctcccagtcaatcatgttttgctcgcatatgctatcttttgagtctcttcctaaactcatagaataagcacgttggttttttccaccgtcctcctcgtgaacaaaagtacaattacattttagcaaattgaaaataaccacgtggatggaccatattatatgtgatcatattgcttgtcgtcttcgttttcttttaaatgtttacaccactacttcctgacacgtgtccctattcacatcatccttgttatatcgttttactTATAaaggatcacgaacaccaaaacatcaatgtgtacgtcttttgcataagaagaaacagagagcattatcaattattaacaattacacaagacagcga 3′-aATG The promoter was cloned from theorganism:   Arabidopsis thaliana, Columbia ecotype Alternativenucleotides: Predicted Position (bp) Mismatch Predicted/Experimental  5PCR error or ecotype variant SNP g/— correct is —/— 17 PCR error orecotype variant SNP c/— correct is —/— The promoter was cloned in thevector:  pNewbin4-HAP1-GFP When cloned into the vector the promoter wasoperably linked to a marker, which was the type: GFP-ER Promoter-markervector was tested in: Arabidopsis thaliana, WS ecotype Generationscreened:   XT1 Mature   XT2 Seedling   T2 Mature   T3 Seedling Thespatial expression of the promoter-marker vector was found observed inand would be useful in expression in any or all of the following: FlowerH pedicel H receptacle H sepal H petal H filament H anther H carpel Hstigma Hepidermis Hstomata H silique H style Silique H stigma H style Hcarpel H septum H placentae H epidermis Stem L epidermis L cortex Hstomata Leaf H mesophyll H stomata Hypocotyl H epidermis H stomataCotyledon H mesophyll H epidermis Rosette Leaf H mesophyll H epidermisPrimary Root H epidermis Observed expression pattern: T1 mature: Highexpression throughout floral organs. High expression in stem guard cellsand cortex cells surrounding stomal chamber (see Table 1. FIG. P). Notexpressed in shoot apical meristem, early flower primordia, pollen andovules. T2 seedling: Expressed in all tissues near seedling apexincreasing toward root. High root epidermis expression. OptionalPromoter Fragments: 5′ UTR region at base pairs 905-1000. Misc. promoterinformation:   Bidirectionality: Pass  Exons: Pass    Repeats: No TheCeres cDNA ID of the endogenous coding sequence to the promoter:12462179 cDNA nucleotide sequence:AATGTGTACGTCTTTTGCATAAGAAGAAACAGAGAGCATTATCAATTATTAACAATTACACAAGACAGCGAGATTGTAAAAGAGTAAGAGAGAGAGAATGGCAGGAGAGGCAGAGGCTTTGGCCACGACGGCACCGTTAGCTCCGGTCACCAGTCAGCGAAAAGTACGGAACGATTTGGAGGAAACATTACCAAAACCATACATGGCAAGAGCATTAGCAGCTCCAGATACAGAGCATCCGAATGGAACAGAAGGTCACGATAGCAAAGGAATGAGTGTTATGCAACAACATGTTGCTTTCTTCGACCAAAACGACGATGGAATCGTCTATCCTTGGGAGACTTATAAGGGATTTCGTGACCTTGGTTTCAACCCAATTTCCTCTATCTTTTGGACCTTACTCATAAACTTAGCGTTCAGCTACGTTACACTTCCGAGTTGGGTGCCATCACCATTATTGCCGGTTTATATCGACAACATACACAAAGCCAAGCATGGGAGTGATTCGAGCACCTATGACACCGAAGGAAGGTATGTCCCAGTTAACCTCGAGAACATATTTAGCAAATACGCGCTAACGGTTAAAGATAAGTTATCATTTAAAGAGGTTTGGAATGTAACCGAGGGAAATCGAATGGCAATCGATCCTTTTGGATGGCTTTCAAACAAAGTTGAATGGATACTACTCTATATTCTTGCTAAGGACGAAGATGGTTTCCTATCTAAAGAAGCTGTGAGAGGTTGCTTTGATGGAAGTTTATTTGAACAAATTGCCAAAGAGAGGGCCAATTCTCGCAAACAAGACTAAGAATGTGTGTGTTTGGTTAGCGAATAAAGCTTTTTGAAGAAAAGCATTGTGTAATTTAGCTTCTTTCGTCTTGTTATTCAGTTTGGGGATTTGTATAATTAATGTGTTTGTAAACTATGTTTCAAAGTTATATAAATAAGAGAAGATGTTACAAAAAAAAAAAAAAGACTAATAAGAAGAATTTGGT Coding sequence:MAGEAEALATTAPLAPVTSQRKVRNDLEETLPKPYMARALAAPDTEHPNGTEGHDSKGMSVMQQHVAFFDQNDDGIVYPWETYKGFRDLGFNPISSIFWTLLINLAFSYVTLPSWVPSPLLPVYIDNIHKAKHGSDSSTYDTEGRYVPVNLENIFSKYALTVKDKLSFKEVWNVTEGNRMAIDPFGWLSNKVEWILLYILAKDEDGFLSKEAVRGCFDGSLFEQIAKERANSRKQD* Microarray data shows thatthe coding sequence was expressed in the following experiments, whichshows that the promoter would be useful to modulate expression insituations similar to the following: CDNA_ID SHORT_NAME EXPT_REP_IDIS_UP 12462179 At_100uM_ABA 20000166 + 12462179 At_100uM_ABA 20000169 +12462179 At_2mM_SA 20000182 + 12462179 At_Shoots 20000184 − 12462179At_Roots 20000185 − 12462179 At_0.001percent_MeJA 20000211 + 12462179At_Open_Flower 20000264 + 12462179 At_Open_Flower 20000265 + 12462179At_100mM_NaCl 20000268 + 12462179 At_100mM_NaCl 20000308 + 12462179At_Pollen 20000326 − 12462179 At_Drought 20000436 + 12462179 At_Drought20000437 + 12462179 At_Shoots 20000438 − 12462179 At_Roots 20000439 −12462179 At_100uM_NAA 20000445 + 12462179 At_100uM_ABA 20000453 +12462179 At_100uM_ABA 20000455 + 12462179 At_42deg_Heat 20000458 +12462179 At_Wounding 20000506 + 12462179 At_100uM_ABA_Mutants 20000575 +12462179 At_100uM_ABA_Mutants 20000576 + 12462179 At_Herbicide_Mutants20000640 − 12462179 At_Herbicide_Mutants 20000642 − 12462179At_15mM_NH4NO3_L-to-H 20000709 − 12462179 At_Petals 20000794 + 12462179At_Line_Comparisons 20001151 + 12462179 At_Line_Comparisons 20001184 +12462179 At_Far-red-induction 20001248 − 12462179 At_Line_Comparisons20001307 + 12462179 At_Line_Comparisons 20001310 − 12462179At_Interploidy_Crosses 20001316 − 12462179 At_Line_Comparisons20001319 + 12462179 At_Line_Comparisons 20001347 + 12462179At_Far-red-induction 20001451 + 12462179 At_Far-red-enriched 20001504 +12462179 At_Drought_Soil_Dry 20001553 + 12462179 At_Drought_Soil_Dry20001554 + 12462179 At_Drought_Soil_Dry 20001555 + 12462179At_Drought_Soil_Dry 20001556 + 12462179 At_Drought_Soil_Dry 20001559 +12462179 At_Interploidy_Crosses 20001654 + 12462179At_50mM_NH4NO3_L-to-H 20001757 − 12462179 At_Far-red-enriched-adult20001768 + 12462179 At_Far-red-enriched-adult 20001770 + 12462179At_Far-red-enriched-adult 20001771 + 12462179 At_Far-red-enriched-adult20001774 + 12462179 At_Drought_Reproduction 20001904 + 12462179At_Drought_Reproduction 20001905 + 12462179 At_Drought_Reproduction20001906 + 12462179 At_Drought_Reproduction 20001908 + 12462179At_Drought_Reproduction 20001910 + 12462179 At_Drought_Reproduction20001911 + 12462179 At_8deg_Cold 20002107 − 12462179 At_8deg_Cold20002108 − 12462179 At_8deg_Cold 20002109 − The parameters for themicroarray experiments listed above by Expt_Rep_ID and Short_Name are asfollow below: CDNA_ID SHORT_NAME EXPT_REP_ID PARAM_NAME VALUE 12462179At_100uM_ABA 20000166 Timepoint (hr) 1 12462179 At_100uM_ABA 20000166Age (day) 14 12462179 At_100uM_ABA 20000166 Treatment 100 uM ABA vs. NoTreatment 12462179 At_100uM_ABA 20000166 Organism A. thaliana 12462179At_100uM_ABA 20000166 Tissue Aerial 12462179 At_100uM_ABA 20000166 PlantLine WS 12462179 At_100uM_ABA 20000169 Timepoint (hr) 6 12462179At_100uM_ABA 20000169 Age (day) 14 12462179 At_100uM_ABA 20000169Treatment 100 uM ABA vs. No Treatment 12462179 At_100uM_ABA 20000169Organism A. thaliana 12462179 At_100uM_ABA 20000169 Tissue Aerial12462179 At_100uM_ABA 20000169 Plant Line WS 12462179 At_2mM_SA 20000182Timepoint (hr) 6 12462179 At_2mM_SA 20000182 Age (day) 14 12462179At_2mM_SA 20000182 Treatment 2 mM SA vs. No Treatment 12462179 At_2mM_SA20000182 Organism A. thaliana 12462179 At_2mM_SA 20000182 Tissue Aerial12462179 At_2mM_SA 20000182 Plant Line WS 12462179 At_Shoots 20000184Age (day) 7 vs. 21 12462179 At_Shoots 20000184 Organism A. thaliana12462179 At_Shoots 20000184 Tissue Shoots vs. Whole Plant 12462179At_Shoots 20000184 Plant Line WS 12462179 At_Roots 20000185 Age (day) 7vs. 21 12462179 At_Roots 20000185 Organism A. thaliana 12462179 At_Roots20000185 Tissue Roots vs. Whole Plant 12462179 At_Roots 20000185 PlantLine WS 12462179 At_0.001percent_MeJA 20000211 Timepoint (hr) 1 12462179At_0.001percent_MeJA 20000211 Age (day) 14 12462179 At_0.001percent_MeJA20000211 Treatment 0.001 percent MeJA vs. No Treatment 12462179At_0.001percent_MeJA 20000211 Organism A. thaliana 12462179At_0.001percent_MeJA 20000211 Tissue Aerial 12462179At_0.001percent_MeJA 20000211 Plant Line WS 12462179 At_Open_Flower20000264 Age (day) 21 12462179 At_Open_Flower 20000264 Organism A.thaliana 12462179 At_Open_Flower 20000264 Tissue Open Flower vs. WholePlant 12462179 At_Open_Flower 20000264 Plant Line WS 12462179At_Open_Flower 20000265 Age (day) 21 12462179 At_Open_Flower 20000265Organism A. thaliana 12462179 At_Open_Flower 20000265 Tissue ClosedFlower vs. Whole Plant 12462179 At_Open_Flower 20000265 Plant Line WS12462179 At_100mM_NaCl 20000268 Timepoint (hr) 6 12462179 At_100mM_NaCl20000268 Age (day) 14 12462179 At_100mM_NaCl 20000268 Treatment 100 mMNaCl vs. No Treatment 12462179 At_100mM_NaCl 20000268 Organism A.thaliana 12462179 At_100mM_NaCl 20000268 Tissue Whole Plant 12462179At_100mM_NaCl 20000268 Plant Line WS 12462179 At_100mM_NaCl 20000308 Age(day) 17 12462179 At_100mM_NaCl 20000308 Timepoint (hr) 72 12462179At_100mM_NaCl 20000308 Treatment 100 mM NaCl vs. No Treatment 12462179At_100mM_NaCl 20000308 Organism A. thaliana 12462179 At_100mM_NaCl20000308 Tissue Whole Plant 12462179 At_100mM_NaCl 20000308 Plant LineWS 12462179 At_Pollen 20000326 Age (day) 0 vs. 21 12462179 At_Pollen20000326 Organism A. thaliana 12462179 At_Pollen 20000326 Tissue Pollenvs. Whole Plant 12462179 At_Pollen 20000326 Plant Line WS 12462179At_Drought 20000436 Age (day) 7 12462179 At_Drought 20000436 Timepoint(hr) 12 12462179 At_Drought 20000436 Organism A. thaliana 12462179At_Drought 20000436 Treatment Drought vs. No Drought 12462179 At_Drought20000436 Tissue Whole Plant 12462179 At_Drought 20000436 Plant Line WS12462179 At_Drought 20000437 Age (day) 8 12462179 At_Drought 20000437Timepoint (hr) 24 12462179 At_Drought 20000437 Organism A. thaliana12462179 At_Drought 20000437 Treatment Drought vs. No Drought 12462179At_Drought 20000437 Tissue Whole Plant 12462179 At_Drought 20000437Plant Line WS 12462179 At_Shoots 20000438 Age (day) 14 vs. 21 12462179At_Shoots 20000438 Organism A. thaliana 12462179 At_Shoots 20000438Tissue Shoots vs. Whole Plant 12462179 At_Shoots 20000438 Plant Line WS12462179 At_Roots 20000439 Age (day) 14 vs. 21 12462179 At_Roots20000439 Organism A. thaliana 12462179 At_Roots 20000439 Tissue Rootsvs. Whole Plant 12462179 At_Roots 20000439 Plant Line WS 12462179At_100uM_NAA 20000445 Timepoint (hr) 6 12462179 At_100uM_NAA 20000445Age (day) 14 12462179 At_100uM_NAA 20000445 Treatment 100 uM NAA vs. NoTreatment 12462179 At_100uM_NAA 20000445 Organism A. thaliana 12462179At_100uM_NAA 20000445 Tissue Aerial 12462179 At_100uM_NAA 20000445 PlantLine WS 12462179 At_100uM_ABA 20000453 Age (day) 15 12462179At_100uM_ABA 20000453 Timepoint (hr) 24 12462179 At_100uM_ABA 20000453Treatment 100 uM ABA vs. No Treatment 12462179 At_100uM_ABA 20000453Organism A. thaliana 12462179 At_100uM_ABA 20000453 Tissue Aerial12462179 At_100uM_ABA 20000453 Plant Line WS 12462179 At_100uM_ABA20000455 Age (day) 16 12462179 At_100uM_ABA 20000455 Timepoint (hr) 4812462179 At_100uM_ABA 20000455 Treatment 100 uM ABA vs. No Treatment12462179 At_100uM_ABA 20000455 Organism A. thaliana 12462179At_100uM_ABA 20000455 Tissue Aerial 12462179 At_100uM_ABA 20000455 PlantLine WS 12462179 At_42deg_Heat 20000458 Timepoint (hr) 8 12462179At_42deg_Heat 20000458 Age (day) 14 12462179 At_42deg_Heat 20000458Temperature (deg C.) 42 vs. 22 12462179 At_42deg_Heat 20000458 OrganismA. thaliana 12462179 At_42deg_Heat 20000458 Tissue Aerial 12462179At_42deg_Heat 20000458 Plant Line WS 12462179 At_Wounding 20000506Timepoint (hr) 6 12462179 At_Wounding 20000506 Age (day) 14 12462179At_Wounding 20000506 Organism A. thaliana 12462179 At_Wounding 20000506Tissue Aerial 12462179 At_Wounding 20000506 Treatment Wounding vs. NoWounding 12462179 At_Wounding 20000506 Plant Line WS 12462179At_100uM_ABA_Mutants 20000575 Timepoint (hr) 6 12462179At_100uM_ABA_Mutants 20000575 Treatment 1 uM ABA vs. No Treatment12462179 At_100uM_ABA_Mutants 20000575 Organism A. thaliana 12462179At_100uM_ABA_Mutants 20000575 Plant Line CS22 12462179At_100uM_ABA_Mutants 20000575 Tissue Whole Plant 12462179At_100uM_ABA_Mutants 20000576 Timepoint (hr) 6 12462179At_100uM_ABA_Mutants 20000576 Treatment 1 uM ABA vs. No Treatment12462179 At_100uM_ABA_Mutants 20000576 Organism A. thaliana 12462179At_100uM_ABA_Mutants 20000576 Plant Line CS23 12462179At_100uM_ABA_Mutants 20000576 Tissue Whole Plant 12462179At_Herbicide_Mutants 20000640 Timepoint (hr) 12 12462179At_Herbicide_Mutants 20000640 Plant Line 05377RR/BR27173 12462179At_Herbicide_Mutants 20000640 Treatment Roundup vs. No Treatment12462179 At_Herbicide_Mutants 20000640 Tissue Seedlings 12462179At_Herbicide_Mutants 20000642 Timepoint (hr) 12 12462179At_Herbicide_Mutants 20000642 Plant Line 3950BR/PCJE10000 12462179At_Herbicide_Mutants 20000642 Treatment Finale vs. No Treatment 12462179At_Herbicide_Mutants 20000642 Tissue Seedlings 12462179At_15mM_NH4NO3_L-to-H 20000709 Timepoint (hr) 4 12462179At_15mM_NH4NO3_L-to-H 20000709 Age (hr) 14 12462179At_15mM_NH4NO3_L-to-H 20000709 Treatment 15 mM NH4NO3 vs. 30 mM Mannitol12462179 At_15mM_NH4NO3_L-to-H 20000709 Organism A. thaliana 12462179At_15mM_NH4NO3_L-to-H 20000709 Tissue Aerial 12462179At_15mM_NH4NO3_L-to-H 20000709 Plant Line WS 12462179 At_Petals 20000794Age (day) 23-25 days 12462179 At_Petals 20000794 Organism A. thaliana12462179 At_Petals 20000794 Tissue Petals vs. Whole plant 12462179At_Petals 20000794 Plant Line WS 12462179 At_Line_Comparisons 20001151Plant Line ME01339-01 vs. WS 12462179 At_Line_Comparisons 20001184 PlantLine ME01848-01 vs. WS 12462179 At_Far-red-induction 20001248 Timepoint(hr) 4 12462179 At_Far-red-induction 20001248 Age (day) 7 12462179At_Far-red-induction 20001248 Organism A. thaliana 12462179At_Far-red-induction 20001248 Plant Line Columbia 12462179At_Far-red-induction 20001248 Light Far-red vs. White 12462179At_Far-red-induction 20001248 Tissue Whole Plant 12462179At_Line_Comparisons 20001307 Plant Line WBin4-WX2-A vs. WS 12462179At_Line_Comparisons 20001310 Plant Line WBin4-WX17-A vs. WS 12462179At_Interploidy_Crosses 20001316 Age (day) 5 12462179At_Interploidy_Crosses 20001316 Organism A. thaliana 12462179At_Interploidy_Crosses 20001316 Plant Line Columbia 12462179At_Interploidy_Crosses 20001316 Cross hemi × 2X vs. 2X × 2X 12462179At_Interploidy_Crosses 20001316 Tissue Siliques 12462179At_Line_Comparisons 20001319 Plant Line WBin4-WX24-A vs. WS 12462179At_Line_Comparisons 20001347 Plant Line ME01604-01 vs. WS 12462179At_Far-red-induction 20001451 Age (day) 8 12462179 At_Far-red-induction20001451 Timepoint (hr) 24 12462179 At_Far-red-induction 20001451Organism A. thaliana 12462179 At_Far-red-induction 20001451 Plant LineColumbia 12462179 At_Far-red-induction 20001451 Light Far-red vs. White12462179 At_Far-red-induction 20001451 Tissue Whole Plant 12462179At_Far-red-enriched 20001504 Timepoint (day) 6 12462179At_Far-red-enriched 20001504 Age (day) 10 12462179 At_Far-red-enriched20001504 Organism A. thaliana 12462179 At_Far-red-enriched 20001504Plant Line Columbia 12462179 At_Far-red-enriched 20001504 Light Far-redenriched vs. White 12462179 At_Far-red-enriched 20001504 Tissue WholePlant 12462179 At_Drought_Soil_Dry 20001553 Timepoint (day) 5 12462179At_Drought_Soil_Dry 20001553 Age (day) 19 12462179 At_Drought_Soil_Dry20001553 Organism A. thaliana 12462179 At_Drought_Soil_Dry 20001553Treatment Drought vs. No Drought 12462179 At_Drought_Soil_Dry 20001553Post Timepoint (hr) None 12462179 At_Drought_Soil_Dry 20001553Post-Treatment None 12462179 At_Drought_Soil_Dry 20001553 Plant Line WS12462179 At_Drought_Soil_Dry 20001554 Timepoint (day) 7 12462179At_Drought_Soil_Dry 20001554 Age (day) 21 12462179 At_Drought_Soil_Dry20001554 Organism A. thaliana 12462179 At_Drought_Soil_Dry 20001554Treatment Drought vs. No Drought 12462179 At_Drought_Soil_Dry 20001554Post Timepoint (hr) None 12462179 At_Drought_Soil_Dry 20001554Post-Treatment None 12462179 At_Drought_Soil_Dry 20001554 Plant Line WS12462179 At_Drought_Soil_Dry 20001555 Timepoint (day) 10 12462179At_Drought_Soil_Dry 20001555 Age (day) 24 12462179 At_Drought_Soil_Dry20001555 Organism A. thaliana 12462179 At_Drought_Soil_Dry 20001555Treatment Drought vs. No Drought 12462179 At_Drought_Soil_Dry 20001555Post Timepoint (hr) None 12462179 At_Drought_Soil_Dry 20001555Post-Treatment None 12462179 At_Drought_Soil_Dry 20001555 Plant Line WS12462179 At_Drought_Soil_Dry 20001556 Timepoint (day) 12 12462179At_Drought_Soil_Dry 20001556 Age (day) 26 12462179 At_Drought_Soil_Dry20001556 Organism A. thaliana 12462179 At_Drought_Soil_Dry 20001556Treatment Drought vs. No Drought 12462179 At_Drought_Soil_Dry 20001556Post Timepoint (hr) None 12462179 At_Drought_Soil_Dry 20001556Post-Treatment None 12462179 At_Drought_Soil_Dry 20001556 Plant Line WS12462179 At_Drought_Soil_Dry 20001559 Timepoint (day) 14 12462179At_Drought_Soil_Dry 20001559 Age (day) 28 12462179 At_Drought_Soil_Dry20001559 Post Timepoint (hr) 29 12462179 At_Drought_Soil_Dry 20001559Organism A. thaliana 12462179 At_Drought_Soil_Dry 20001559 TreatmentDrought vs. No Drought 12462179 At_Drought_Soil_Dry 20001559Post-Treatment Re-Water vs. No Drought 12462179 At_Drought_Soil_Dry20001559 Plant Line WS 12462179 At_Interploidy_Crosses 20001654 Age(day) 5 12462179 At_Interploidy_Crosses 20001654 Cross 6X × 2X vs. 2X× 2X 12462179 At_Interploidy_Crosses 20001654 Organism A. thaliana12462179 At_Interploidy_Crosses 20001654 Plant Line Columbia 12462179At_Interploidy_Crosses 20001654 Tissue Siliques 12462179At_50mM_NH4NO3_L-to-H 20001757 Timepoint (hr) 6 12462179At_50mM_NH4NO3_L-to-H 20001757 Treatment 50 mM NH4NO3 vs 100 mM Mannitol12462179 At_50mM_NH4NO3_L-to-H 20001757 Tissue Leaf 12462179At_Far-red-enriched-adult 20001768 Timepoint (hr) 1 12462179At_Far-red-enriched-adult 20001768 Age (day) 28 12462179At_Far-red-enriched-adult 20001768 Organism A. thaliana 12462179At_Far-red-enriched-adult 20001768 Tissue Aerial 12462179At_Far-red-enriched-adult 20001768 Plant Line Columbia 12462179At_Far-red-enriched-adult 20001768 Light Far-red enriched vs. White12462179 At_Far-red-enriched-adult 20001770 Timepoint (hr) 8 12462179At_Far-red-enriched-adult 20001770 Age (day) 28 12462179At_Far-red-enriched-adult 20001770 Organism A. thaliana 12462179At_Far-red-enriched-adult 20001770 Tissue Aerial 12462179At_Far-red-enriched-adult 20001770 Plant Line Columbia 12462179At_Far-red-enriched-adult 20001770 Light Far-red enriched vs. White12462179 At_Far-red-enriched-adult 20001771 Timepoint (hr) 16 12462179At_Far-red-enriched-adult 20001771 Age (day) 28 12462179At_Far-red-enriched-adult 20001771 Organism A. thaliana 12462179At_Far-red-enriched-adult 20001771 Tissue Aerial 12462179At_Far-red-enriched-adult 20001771 Plant Line Columbia 12462179At_Far-red-enriched-adult 20001771 Light Far-red enriched vs. White12462179 At_Far-red-enriched-adult 20001774 Age (day) 31 12462179At_Far-red-enriched-adult 20001774 Timepoint (hr) 72 12462179At_Far-red-enriched-adult 20001774 Organism A. thaliana 12462179At_Far-red-enriched-adult 20001774 Tissue Aerial 12462179At_Far-red-enriched-adult 20001774 Plant Line Columbia 12462179At_Far-red-enriched-adult 20001774 Light Far-red enriched vs. White12462179 At_Drought_Reproduction 20001904 Timepoint (day) 7 12462179At_Drought_Reproduction 20001904 Age (day) 37 12462179At_Drought_Reproduction 20001904 Organism A. thaliana 12462179At_Drought_Reproduction 20001904 Treatment Drought vs. No Drought12462179 At_Drought_Reproduction 20001904 Tissue Rosettes 12462179At_Drought_Reproduction 20001904 Plant Line WS 12462179At_Drought_Reproduction 20001905 Timepoint (day) 10 12462179At_Drought_Reproduction 20001905 Age (day) 40 12462179At_Drought_Reproduction 20001905 Organism A. thaliana 12462179At_Drought_Reproduction 20001905 Treatment Drought vs. No Drought12462179 At_Drought_Reproduction 20001905 Tissue Rosettes 12462179At_Drought_Reproduction 20001905 Plant Line WS 12462179At_Drought_Reproduction 20001906 Timepoint (day) 5 12462179At_Drought_Reproduction 20001906 Age (day) 35 12462179At_Drought_Reproduction 20001906 Organism A. thaliana 12462179At_Drought_Reproduction 20001906 Treatment Drought vs. No Drought12462179 At_Drought_Reproduction 20001906 Tissue Siliques 12462179At_Drought_Reproduction 20001906 Plant Line WS 12462179At_Drought_Reproduction 20001908 Timepoint (day) 10 12462179At_Drought_Reproduction 20001908 Age (day) 40 12462179At_Drought_Reproduction 20001908 Organism A. thaliana 12462179At_Drought_Reproduction 20001908 Treatment Drought vs. No Drought12462179 At_Drought_Reproduction 20001908 Tissue Siliques 12462179At_Drought_Reproduction 20001908 Plant Line WS 12462179At_Drought_Reproduction 20001910 Timepoint (day) 7 12462179At_Drought_Reproduction 20001910 Age (day) 37 12462179At_Drought_Reproduction 20001910 Organism A. thaliana 12462179At_Drought_Reproduction 20001910 Treatment Drought vs. No Drought12462179 At_Drought_Reproduction 20001910 Tissue Flowers 12462179At_Drought_Reproduction 20001910 Plant Line WS 12462179At_Drought_Reproduction 20001911 Timepoint (day) 10 12462179At_Drought_Reproduction 20001911 Age (day) 40 12462179At_Drought_Reproduction 20001911 Organism A. thaliana 12462179At_Drought_Reproduction 20001911 Treatment Drought vs. No Drought12462179 At_Drought_Reproduction 20001911 Tissue Flowers 12462179At_Drought_Reproduction 20001911 Plant Line WS 12462179 At_8deg_Cold20002107 Age (day) 11 12462179 At_8deg_Cold 20002107 Timepoint (hr) 9612462179 At_8deg_Cold 20002107 Temperature (deg C.) 8 vs. 22 12462179At_8deg_Cold 20002107 Organism A. thaliana 12462179 At_8deg_Cold20002107 Tissue Whole Plant 12462179 At_8deg_Cold 20002107 Plant Line WS12462179 At_8deg_Cold 20002108 Age (day) 14 12462179 At_8deg_Cold20002108 Timepoint (hr) 168 12462179 At_8deg_Cold 20002108 Temperature(deg C.) 8 vs. 22 12462179 At_8deg_Cold 20002108 Organism A. thaliana12462179 At_8deg_Cold 20002108 Tissue Whole Plant 12462179 At_8deg_Cold20002108 Plant Line WS 12462179 At_8deg_Cold 20002109 Age (day) 1612462179 At_8deg_Cold 20002109 Timepoint (hr) 216 12462179 At_8deg_Cold20002109 Temperature (deg C.) 8 vs. 22 12462179 At_8deg_Cold 20002109Organism A. thaliana 12462179 At_8deg_Cold 20002109 Tissue Whole Plant12462179 At_8deg_Cold 20002109 Plant Line WS 13613778 At_Root_Tips108434 Tissue Root Tips 13613778 At_20uM_KNO3_H-to-L 108455 Timepoint(hr) 1 13613778 At_20uM_KNO3_H-to-L 108455 Treatment 20 uM KNO3 vs. 50mM KNO3 13613778 At_5-1-F2-137 108460 Plant Line 5-1-F2-137(mutant)13613778 At_5-1-F2-137 108460 Probe Method Amplified 13613778At_5-1-F2-137 108460 Tissue Inflorescences 13613778 At_Germinating_Seeds108464 Age (day) 4 vs. 0 13613778 At_Germinating_Seeds 108464 TissueGerminating Seeds 13613778 At_Shoot_Apices 108480 Treatment 1uM BR vs.No Treatment 13613778 At_Shoot_Apices 108480 Plant Line Ws-2 13613778At_Shoot_Apices 108481 Treatment 1uM BRZ vs. No Treatment 13613778At_Shoot_Apices 108481 Plant Line Ws-2 13613778 At_15mM_NH4NO3_L-to-108487 Timepoint (hr) 0.5 H_Rosette 13613778 At_15mM_NH4NO3_L-to- 108487Treatment 15 mM NH4NO3 vs. 30 mM Mannitol H_Rosette 13613778At_15mM_NH4NO3_L-to- 108487 Tissue Rosette H_Rosette 13613778At_15mM_NH4NO3_L-to- 108488 Timepoint (hr) 2 H_Rosette 13613778At_15mM_NH4NO3_L-to- 108488 Treatment 15 mM NH4NO3 vs. 30 mM MannitolH_Rosette 13613778 At_15mM_NH4NO3_L-to- 108488 Tissue Rosette H_Rosette13613778 At_ap2_floral_buds 108501 Plant Line ap2 (Ler.) 13613778At_ap2_floral_buds 108501 Tissue Closed Flower 13613778 At_42deg_Heat108577 Timepoint (hr) 6 13613778 At_42deg_Heat 108577 Temperature 42 vs.22 (deg C.) 13613778 At_42deg_Heat 108577 Tissue Aerial 13613778At_4deg_Cold 108578 Timepoint (hr) 1 13613778 At_4deg_Cold 108578Temperature 4 vs. 22 (deg C.) 13613778 At_4deg_Cold 108578 Tissue Aerial13613778 At_4deg_Cold 108579 Timepoint (hr) 6 13613778 At_4deg_Cold108579 Temperature 4 vs. 22 (deg C.) 13613778 At_4deg_Cold 108579 TissueAerial 13613778 At_5mM_NaNP 108584 Timepoint (hr) 1 13613778 At_5mM_NaNP108584 Treatment 5 mM sodium nitroprusside vs. No Treatment 13613778At_5mM_NaNP 108584 Tissue Aerial 13613778 At_5mM_NaNP 108585 Timepoint(hr) 6 13613778 At_5mM_NaNP 108585 Treatment 5 mM sodium nitroprussidevs. No Treatment 13613778 At_5mM_NaNP 108585 Tissue Aerial 13613778At_2mM_SA 108586 Timepoint (hr) 1 13613778 At_2mM_SA 108586 Treatment 2mM SA vs. No Treatment 13613778 At_2mM_SA 108586 Tissue Aerial 13613778At_2mM_SA 108587 Timepoint (hr) 6 13613778 At_2mM_SA 108587 Treatment 2mM SA vs. No Treatment 13613778 At_2mM_SA 108587 Tissue Aerial 13613778At_15mM_NH4NO3_L-to-H 108588 Timepoint (hr) 2 13613778At_15mM_NH4NO3_L-to-H 108588 Treatment 15 mM NH4NO3 vs. 30 mM Mannitol13613778 At_15mM_NH4NO3_L-to-H 108588 Tissue Aerial 13613778At_Ler-pi_Ovule 108595 Plant Line Ler_pi 13613778 At_Ler-pi_Ovule 108595Tissue Ovules 13613778 At_100uM_ABA 108606 Timepoint (hr) 2 13613778At_100uM_ABA 108606 Treatment 100 uM ABA vs. No Treatment 13613778At_100uM_ABA 108606 Tissue Aerial 13613778 At_2mM_SA 108667 Timepoint(hr) 1 13613778 At_2mM_SA 108667 Treatment 2 mM SA vs. No Treatment13613778 At_2mM_SA 108667 Plant Line WS 13613778 At_100uM_ABA_Mutants20000069 Timepoint (hr) 6 13613778 At_100uM_ABA_Mutants 20000069Treatment 100 uM ABA vs. No Treatment 13613778 At_100uM_ABA_Mutants20000069 Tissue Aerial 13613778 At_100uM_ABA_Mutants 20000069 Plant LineCS23 13613778 At_100uM_ABA_Mutants 20000071 Timepoint (hr) 6 13613778At_100uM_ABA_Mutants 20000071 Treatment 100 uM ABA vs. No Treatment13613778 At_100uM_ABA_Mutants 20000071 Tissue Aerial 13613778At_100uM_ABA_Mutants 20000071 Plant Line CS8104 13613778At_100uM_ABA_Mutants 20000086 Timepoint (hr) 6 13613778At_100uM_ABA_Mutants 20000086 Treatment 100 uM ABA vs. No Treatment13613778 At_100uM_ABA_Mutants 20000086 Tissue Aerial 13613778At_100uM_ABA_Mutants 20000086 Plant Line CS22 13613778At_100uM_ABA_Mutants 20000087 Timepoint (hr) 6 13613778At_100uM_ABA_Mutants 20000087 Treatment 100 uM ABA vs. No Treatment13613778 At_100uM_ABA_Mutants 20000087 Tissue Aerial 13613778At_100uM_ABA_Mutants 20000087 Plant Line WS 13613778 At_2mM_SA_CS3726-20000091 Timepoint (hr) 0 Columbia 13613778 At_2mM_SA_CS3726- 20000091Tissue Aerial Columbia 13613778 At_2mM_SA_CS3726- 20000091 Plant LineCS3726 vs. Columbia Columbia 13613778 At_2mM_SA_CS3726- 20000091Treatment None Columbia 13613778 At_100uM_ABA_Mutants 20000117 Timepoint(hr) 6 13613778 At_100uM_ABA_Mutants 20000117 Treatment 100 uM ABA vs.No Treatment 13613778 At_100uM_ABA_Mutants 20000117 Tissue Aerial13613778 At_100uM_ABA_Mutants 20000117 Plant Line Columbia 13613778At_42deg_Heat 20000144 Timepoint (hr) 1 13613778 At_42deg_Heat 20000144Temperature 42 vs. 22 (deg C.) 13613778 At_42deg_Heat 20000144 TissueAerial 13613778 At_42deg_Heat 20000171 Timepoint (hr) 1 13613778At_42deg_Heat 20000171 Age (day) 14 13613778 At_42deg_Heat 20000171Temperature 42 vs. 22 (deg C.) 13613778 At_42deg_Heat 20000171 OrganismA. thaliana 13613778 At_42deg_Heat 20000171 Tissue Aerial 13613778At_42deg_Heat 20000171 Plant Line WS 13613778 At_42deg_Heat 20000173Timepoint (hr) 6 13613778 At_42deg_Heat 20000173 Age (day) 14 13613778At_42deg_Heat 20000173 Temperature 42 vs. 22 (deg C.) 13613778At_42deg_Heat 20000173 Organism A. thaliana 13613778 At_42deg_Heat20000173 Tissue Aerial 13613778 At_42deg_Heat 20000173 Plant Line WS13613778 At_2mM_SA 20000181 Timepoint (hr) 1 13613778 At_2mM_SA 20000181Age (day) 14 13613778 At_2mM_SA 20000181 Treatment 2 mM SA vs. NoTreatment 13613778 At_2mM_SA 20000181 Organism A. thaliana 13613778At_2mM_SA 20000181 Tissue Aerial 13613778 At_2mM_SA 20000181 Plant LineWS 13613778 At_Shoots 20000184 Age (day) 7 vs. 21 13613778 At_Shoots20000184 Organism A. thaliana 13613778 At_Shoots 20000184 Tissue Shootsvs. Whole Plant 13613778 At_Shoots 20000184 Plant Line WS 13613778At_Roots 20000185 Age (day) 7 vs. 21 13613778 At_Roots 20000185 OrganismA. thaliana 13613778 At_Roots 20000185 Tissue Roots vs. Whole Plant13613778 At_Roots 20000185 Plant Line WS 13613778 At_4deg_Cold 20000213Timepoint (hr) 2 13613778 At_Siliques 20000234 Age (day) 21 13613778At_Siliques 20000234 Tissue <5 mm Siliques vs. Whole Plant 13613778At_Siliques 20000234 Organism A. thaliana 13613778 At_Siliques 20000234Plant Line WS 13613778 At_Siliques 20000236 Age (day) 21 13613778At_Siliques 20000236 Tissue >10 mm Siliques vs. Whole Plant 13613778At_Siliques 20000236 Organism A. thaliana 13613778 At_Siliques 20000236Plant Line WS 13613778 At_Open_Flower 20000264 Age (day) 21 13613778At_Open_Flower 20000264 Organism A. thaliana 13613778 At_Open_Flower20000264 Tissue Open Flower vs. Whole Plant 13613778 At_Open_Flower20000264 Plant Line WS 13613778 At_100mM_NaCl 20000268 Timepoint (hr) 613613778 At_100mM_NaCl 20000268 Age (day) 14 13613778 At_100mM_NaCl20000268 Treatment 100 mM NaCl vs. No Treatment 13613778 At_100mM_NaCl20000268 Organism A. thaliana 13613778 At_100mM_NaCl 20000268 TissueWhole Plant 13613778 At_100mM_NaCl 20000268 Plant Line WS 13613778At_Open_Flower 20000286 Age (day) 21 13613778 At_Open_Flower 20000286Organism A. thaliana 13613778 At_Open_Flower 20000286 Tissue Half Openvs. Whole Plant 13613778 At_Open_Flower 20000286 Plant Line WS 13613778At_Pollen 20000326 Age (day) 0 vs. 21 13613778 At_Pollen 20000326Organism A. thaliana 13613778 At_Pollen 20000326 Tissue Pollen vs. WholePlant 13613778 At_Pollen 20000326 Plant Line WS 13613778 At_Shoots20000438 Age (day) 14 vs. 21 13613778 At_Shoots 20000438 Organism A.thaliana 13613778 At_Shoots 20000438 Tissue Shoots vs. Whole Plant13613778 At_Shoots 20000438 Plant Line WS 13613778 At_Roots 20000439 Age(day) 14 vs. 21 13613778 At_Roots 20000439 Organism A. thaliana 13613778At_Roots 20000439 Tissue Roots vs. Whole Plant 13613778 At_Roots20000439 Plant Line WS 13613778 At_1uM_BR-BRZ 20000441 Treatment 1 uM BRvs. No Treatment 13613778 At_1uM_BR-BRZ 20000441 Tissue Shoot Apices13613778 At_1uM_BR-BRZ 20000443 Treatment 1 uM BRZ vs. No Treatment13613778 At_1uM_BR-BRZ 20000443 Tissue Shoot Apices 13613778At_42deg_Heat 20000458 Timepoint (hr) 8 13613778 At_42deg_Heat 20000458Age (day) 14 13613778 At_42deg_Heat 20000458 Temperature 42 vs. 22 (degC.) 13613778 At_42deg_Heat 20000458 Organism A. thaliana 13613778At_42deg_Heat 20000458 Tissue Aerial 13613778 At_42deg_Heat 20000458Plant Line WS 13613778 At_10percent_PEG 20000460 Age (day) 12 13613778At_10percent_PEG 20000460 Timepoint (day) 12 13613778 At_10percent_PEG20000460 Treatment 10 percent PEG vs. No Treatment 13613778At_10percent_PEG 20000460 Organism A. thaliana 13613778 At_10percent_PEG20000460 Tissue Whole Plant 13613778 At_10percent_PEG 20000460 PlantLine WS 13613778 At_Guard_Cells 20000495 Harvest Date Aug. 02, 200213613778 At_Guard_Cells 20000495 Organism A. thaliana 13613778At_Guard_Cells 20000495 Tissue Guard Cells vs. Leaves 13613778At_10percent_PEG 20000527 Age (day) 20 13613778 At_10percent_PEG20000527 Timepoint (day) 20 13613778 At_10percent_PEG 20000527 Treatment10 percent PEG vs. No Treatment 13613778 At_10percent_PEG 20000527Organism A. thaliana 13613778 At_10percent_PEG 20000527 Tissue WholePlant 13613778 At_10percent_PEG 20000527 Plant Line WS 13613778At_100uM_ABA_Mutants 20000573 Organism A. thaliana 13613778At_100uM_ABA_Mutants 20000573 Plant Line CS22 vs. Ler wt 13613778At_100uM_ABA_Mutants 20000573 Timepoint (hr) N/A 13613778At_100uM_ABA_Mutants 20000573 Treatment None 13613778At_100uM_ABA_Mutants 20000573 Tissue Whole Plant 13613778At_100uM_ABA_Mutants 20000574 Organism A. thaliana 13613778At_100uM_ABA_Mutants 20000574 Plant Line CS23 vs. Ler wt 13613778At_100uM_ABA_Mutants 20000574 Timepoint (hr) N/A 13613778At_100uM_ABA_Mutants 20000574 Treatment None 13613778At_100uM_ABA_Mutants 20000574 Tissue Whole Plant 13613778At_Herbicide_Mutants 20000640 Timepoint (hr) 12 13613778At_Herbicide_Mutants 20000640 Plant Line 05377RR/BR27173 13613778At_Herbicide_Mutants 20000640 Treatment Roundup vs. No Treatment13613778 At_Herbicide_Mutants 20000640 Tissue Seedlings 13613778At_15mM_NH4NO3_L-to-H 20000709 Timepoint (hr) 4 13613778At_15mM_NH4NO3_L-to-H 20000709 Age (hr) 14 13613778At_15mM_NH4NO3_L-to-H 20000709 Treatment 15 mM NH4NO3 vs. 30 mM Mannitol13613778 At_15mM_NH4NO3_L-to-H 20000709 Organism A. thaliana 13613778At_15mM_NH4NO3_L-to-H 20000709 Tissue Aerial 13613778At_15mM_NH4NO3_L-to-H 20000709 Plant Line WS 13613778 At_Petals 20000794Age (day) 23-25 days 13613778 At_Petals 20000794 Organism A. thaliana13613778 At_Petals 20000794 Tissue Petals vs. Whole plant 13613778At_Petals 20000794 Plant Line WS 13613778 At_Line_Comparisons 20001151Plant Line ME01339-01 vs. WS 13613778 At_Line_Comparisons 20001184 PlantLine ME01848-01 vs. WS 13613778 At_Line_Comparisons 20001192 Plant LineWBin4-WX13R-A vs. WS 13613778 At_Line_Comparisons 20001195 Plant LineWBin4-WX14-B vs. WS 13613778 At_Far-red-induction 20001247 Timepoint(hr) 1 13613778 At_Far-red-induction 20001247 Age (day) 7 13613778At_Far-red-induction 20001247 Organism A. thaliana 13613778At_Far-red-induction 20001247 Plant Line Columbia 13613778At_Far-red-induction 20001247 Light Far-red vs. White 13613778At_Far-red-induction 20001247 Tissue Whole Plant 13613778At_Far-red-induction 20001248 Timepoint (hr) 4 13613778At_Far-red-induction 20001248 Age (day) 7 13613778 At_Far-red-induction20001248 Organism A. thaliana 13613778 At_Far-red-induction 20001248Plant Line Columbia 13613778 At_Far-red-induction 20001248 Light Far-redvs. White 13613778 At_Far-red-induction 20001248 Tissue Whole Plant13613778 At_Line_Comparisons 20001300 Plant Line ME01338-05 vs. WS13613778 At_Line_Comparisons 20001307 Plant Line WBin4-WX2-A vs. WS13613778 At_Line_Comparisons 20001308 Plant Line WBin4-WX49-C vs. WS13613778 At_Line_Comparisons 20001309 Plant Line WBin4-WX49R-A vs. WS13613778 At_Line_Comparisons 20001310 Plant Line WBin4-WX17-A vs. WS13613778 At_Line_Comparisons 20001318 Plant Line WBin4-WX14R-A vs. WS13613778 At_Line_Comparisons 20001319 Plant Line WBin4-WX24-A vs. WS13613778 At_Line_Comparisons 20001347 Plant Line ME01604-01 vs. WS13613778 At_Line_Comparisons 20001448 Plant Line ME01323-01 vs. WS13613778 At_50mM_NH4NO3_L-to-H 20001458 Timepoint (hr) 2 13613778At_50mM_NH4NO3_L-to-H 20001458 Treatment 50 mM NH4NO3 vs. 100 mM Manitol13613778 At_50mM_NH4NO3_L-to-H 20001458 Organism A. thaliana 13613778At_50mM_NH4NO3_L-to-H 20001458 Tissue Siliques 13613778At_50mM_NH4NO3_L-to-H 20001458 Age (day) Undefined 13613778At_50mM_NH4NO3_L-to-H 20001458 Plant Line WS 13613778At_Drought_Soil_Dry 20001554 Timepoint (day) 7 13613778At_Drought_Soil_Dry 20001554 Age (day) 21 13613778 At_Drought_Soil_Dry20001554 Organism A. thaliana 13613778 At_Drought_Soil_Dry 20001554Treatment Drought vs. No Drought 13613778 At_Drought_Soil_Dry 20001554Post Timepoint None (hr) 13613778 At_Drought_Soil_Dry 20001554Post-Treatment None 13613778 At_Drought_Soil_Dry 20001554 Plant Line WS13613778 At_Drought_Soil_Dry 20001555 Timepoint (day) 10 13613778At_Drought_Soil_Dry 20001555 Age (day) 24 13613778 At_Drought_Soil_Dry20001555 Organism A. thaliana 13613778 At_Drought_Soil_Dry 20001555Treatment Drought vs. No Drought 13613778 At_Drought_Soil_Dry 20001555Post Timepoint None (hr) 13613778 At_Drought_Soil_Dry 20001555Post-Treatment None 13613778 At_Drought_Soil_Dry 20001555 Plant Line WS13613778 At_Drought_Soil_Dry 20001556 Timepoint (day) 12 13613778At_Drought_Soil_Dry 20001556 Age (day) 26 13613778 At_Drought_Soil_Dry20001556 Organism A. thaliana 13613778 At_Drought_Soil_Dry 20001556Treatment Drought vs. No Drought 13613778 At_Drought_Soil_Dry 20001556Post Timepoint None (hr) 13613778 At_Drought_Soil_Dry 20001556Post-Treatment None 13613778 At_Drought_Soil_Dry 20001556 Plant Line WS13613778 At_Drought_Soil_Dry 20001557 Post Timepoint 3 (hr) 13613778At_Drought_Soil_Dry 20001557 Timepoint (day) 13 13613778At_Drought_Soil_Dry 20001557 Age (day) 27 13613778 At_Drought_Soil_Dry20001557 Organism A. thaliana 13613778 At_Drought_Soil_Dry 20001557Treatment Drought vs. No Drought 13613778 At_Drought_Soil_Dry 20001557Post-Treatment Re-Water vs. No Drought 13613778 At_Drought_Soil_Dry20001557 Plant Line WS 13613778 At_Interploidy_Crosses 20001703 Age(day) 5 13613778 At_Interploidy_Crosses 20001703 Cross 2X × 4X vs. 2X× 2X 13613778 At_Interploidy_Crosses 20001703 Organism A. thaliana13613778 At_Interploidy_Crosses 20001703 Plant Line Columbia 13613778At_Interploidy_Crosses 20001703 Tissue Siliques 13613778At_50mM_NH4NO3_L-to-H 20001757 Timepoint (hr) 6 13613778At_50mM_NH4NO3_L-to-H 20001757 Treatment 50 mM NH4NO3 vs 100 mM Mannitol13613778 At_50mM_NH4NO3_L-to-H 20001757 Tissue Leaf 13613778At_Far-red-enriched-adult 20001773 Age (day) 30 13613778At_Far-red-enriched-adult 20001773 Timepoint (hr) 48 13613778At_Far-red-enriched-adult 20001773 Organism A. thaliana 13613778At_Far-red-enriched-adult 20001773 Tissue Aerial 13613778At_Far-red-enriched-adult 20001773 Plant Line Columbia 13613778At_Far-red-enriched-adult 20001773 Light Far-red enriched vs. White13613778 At_Far-red-enriched-adult 20001774 Age (day) 31 13613778At_Far-red-enriched-adult 20001774 Timepoint (hr) 72 13613778At_Far-red-enriched-adult 20001774 Organism A. thaliana 13613778At_Far-red-enriched-adult 20001774 Tissue Aerial 13613778At_Far-red-enriched-adult 20001774 Plant Line Columbia 13613778At_Far-red-enriched-adult 20001774 Light Far-red enriched vs. White13613778 At_Drought_Reproduction 20001904 Timepoint (day) 7 13613778At_Drought_Reproduction 20001904 Age (day) 37 13613778At_Drought_Reproduction 20001904 Organism A. thaliana 13613778At_Drought_Reproduction 20001904 Treatment Drought vs. No Drought13613778 At_Drought_Reproduction 20001904 Tissue Rosettes 13613778At_Drought_Reproduction 20001904 Plant Line WS 13613778At_Drought_Reproduction 20001907 Timepoint (day) 7 13613778At_Drought_Reproduction 20001907 Age (day) 37 13613778At_Drought_Reproduction 20001907 Organism A. thaliana 13613778At_Drought_Reproduction 20001907 Treatment Drought vs. No Drought13613778 At_Drought_Reproduction 20001907 Tissue Siliques 13613778At_Drought_Reproduction 20001907 Plant Line WS 13613778At_Line_Comparisons 20002012 Plant Line SALK_073455 vs. Columbia13613778 At_8deg_Cold 20002108 Age (day) 14 13613778 At_8deg_Cold20002108 Timepoint (hr) 168 13613778 At_8deg_Cold 20002108 Temperature 8vs. 22 (deg C.) 13613778 At_8deg_Cold 20002108 Organism A. thaliana13613778 At_8deg_Cold 20002108 Tissue Whole Plant 13613778 At_8deg_Cold20002108 Plant Line WS 13613778 At_8deg_Cold 20002109 Age (day) 1613613778 At_8deg_Cold 20002109 Timepoint (hr) 216 13613778 At_8deg_Cold20002109 Temperature 8 vs. 22 (deg C.) 13613778 At_8deg_Cold 20002109Organism A. thaliana 13613778 At_8deg_Cold 20002109 Tissue Whole Plant13613778 At_8deg_Cold 20002109 Plant Line WS Promoter YP00374 Modulatesthe gene: Putative cytochrome P450 The GenBank description of the gene:NM_112814 Arabidopsis thaliana cytochrome P450, putative (At3g19270)mRNA, complete cds gi|18402178|ref|NM_112814.1|[18402178] The promotersequence:5′agaagaaactagaaacgttaaacgcatcaaatcaagaaattaaattgaaggtaatttttaacgccgcctttcaaatattcttcctaggagaggctacaagacgcgtatttctttcgaattctccaaaccattaccattttgatatataataccgacatgccgttgataaagtttgtatgcaaatcgttcattgggtatgagcaaatgccatccattggttcttgtaattaaatggtccaaaaatagtttgttcccactactagttactaatttgtatcactctgcaaaataatcatgatataaacgtatgtgctatttctaattaaaactcaaaagtaatcaatgtacaatgcagagatgaccataaaagaacattaaaacactacttccactaaatctatggggtgccttggcaaggcaattgaataaggagaatgcatcaagatgatatagaaaatgctattcagtttataacattaatgttttggcggaaaattttctatatattagacctttctgtaaaaaaaaaaaaatgatgtagaaaatgctattatgtttcaaaaatttcgcactagtataatacggaacattgtagtttacactgctcattaccatgaaaaccaaggcagtatataccaacattaataaactaaatcgcgatttctagcacccccattaattaattttactattatacattctctttgcttctcgaaataataaacttctctatatcattctacataataaataagaaagaaatcgacaagatctaaatttagatctattcagctttttcgcctgagaagccaaaattgtgaatagaagaaagcagtcgtcatcttcccacgtttggacgaaataaaacataacaataataaaataataaatcaaatatataaatccctaatttgtctttattactccacaattttctatgtgtatataTA 3′-tgtatgtttttgttccctattatatcttctagcttctttcttcctcttcttccttaaaaattcatcctccaaaaca ttctatcatcaacgaaacatttcatattaaattaaataataatcgATG The promoter wascloned from the organism: Arabidopsis thaliana Alternative nucleotides:Query = Predicted Subject = Experimental Predicted Position (bp)Mismatch Predicted/Experimental 1-1000 None Identities = 1000/1000(100%) The promoter was cloned in the vector: pNewbin4-HAP1-GFP Whencloned into the vector the promoter was operably linked to a marker,which was the type: GFP-ER Promoter-marker vector was tested in:Generation screened:   XT1 Mature XT2 Seedling   T2 Mature   T3 SeedlingThe spatial expression of the promoter-marker vector was found observedin and would be useful in expression in any or all of the following:Flower M vascular Silique M placenta, M vascular Hypocotyl H vascularCotyledon H vascular, H petiole Primary Root H vascular Observedexpression pattern of the promoter-marker vector was in: T1 mature: GFPexpressed in outer integument of developing ovule primordium. Higherintegument expression at chalazal pole observed through maturity. T2seedling: Medium to low expression in root vascular bundles weakeningtoward hypocotyl. Weak expression in epidermal cells at root transitionzone.. Misc. promoter information:   Bidirectionality: Pass  Exons: Pass   Repeats: No The Ceres cDNA ID of the endogenous coding sequence tothe promoter:: 12370888 cDNA nucleotide sequence:GTATGTTTTTGTTCCCTATTATATCTTCTAGCTTCTTTCTTCCTCTTCTTCCTTAAAAATTCATCCTCCAAAACATTCTATCATCAACGAAACATTTCATATTAAATTAAATAATAATCGATGGCTGAAATTTGGTTCTTGGTTGTACCAATCCTCATCTTATGCTTGCTTTTGGTAAGAGTGATTGTTTCAAAGAAGAAAAAGAACAGTAGAGGTAAGCTTCCTCCTGGTTCCATGGGATGGCCTTACTTAGGAGAGACTCTACAACTCTATTCACAAAACCCCAATGTTTTCTTCACCTCCAAGCAAAAGAGATATGGAGAGATATTCAAAACCCGAATCCTCGGCTATCCATGCGTGATGTTGGCTAGCCCTGAGGCTGCGAGGTTTGTACTTGTGACTCATGCCCATATGTTCAAACCAACTTATCCGAGAAGCAAAGAGAAGCTGATAGGACCCTCTGCACTCTTTTTCCACCAAGGAGATTATCATTCCCATATAAGGAAACTTGTTCAATCCTCTTTCTACCCTGAAACCATCCGTAAACTCATCCCTGATATCGAGCACATTGCCCTTTCTTCCTTACAATCTTGGGCCAATATGCCGATTGTCTCCACCTACCAGGAGATGAAGAAGTTCGCCTTTGATGTGGGTATTCTAGCCATATTTGGACATTTGGAGAGTTCTTACAAAGAGATCTTGAAACATAACTACAATATTGTGGACAAAGGCTACAACTCTTTCCCCATGAGTCTCCCCGGAACATCTTATCACAAAGCTCTCATGGCGAGAAAGCAGCTAAAGACGATAGTAAGCGAGATTATATGCGAAAGAAGAGAGAAAAGGGCCTTGCAAACGGACTTTCTTGGTCATCTACTCAACTTCAAGAACGAAAAAGGTCGTGTGCTAACCCAAGAACAGATTGCAGACAACATCATCGGAGTCCTTTTCGCCGCACAGGACACGACAGCTAGTTGCTTAACTTGGATTCTTAAGTACTTACATGATGATCAGAAACTTCTAGAAGCTGTTAAGGCTGAGCAAAAGGCTATATATGAAGAAAACAGTAGAGAGAAGAAACCTTTAACATGGAGACAAACGAGGAATATGCCACTGACACATAAGGTTATAGTTGAAAGCTTGAGGATGGCAAGCATCATATCCTTCACATTCAGAGAAGCAGTGGTTGATGTTGAATATAAGGGATATTTGATACCTAAGGGATGGAAAGTGATGCCACTGTTTCGGAATATTCATCACAATCCGAAATATTTTTCAAACCCTGAGGTTTTCGACCCATCTAGATTCGAGGTAAATCCGAAGCCGAATACATTCATGCCTTTTGGAAGTGGAGTTCATGCTTGTCCCGGGAACGAACTCGCCAAGTTACAAATTCTTATATTTCTCCACCATTTAGTTTCCAATTTCCGATGGGAAGTGAAGGGAGGAGAGAAAGGAATACAGTACAGTCCATTTCCAATACCTCAAAACGGTCTTCCCGCTACATTTCGTCGACATTCTCTTTAGTTCCTTAAACCTTTGTAGTAATCTTTGTTGTAGTTAGCCAAATCTAATCCAAATTCGATATAAAAAATCCCCTTTCTATTTTTTTTTAAAATCATTGTTGTAGTCTTGAGGGGGTTTAACATGTAACAACTATGATGAAGTAAAATGTCGATTCCGGT Coding sequence:MAEIWFLVVPILILCLLLVRVIVSKKKKNSRGKLPPGSMGWPYLGETLQLYSQNPNVFFTSKQKRYGEIFKTRILGYPCVMLASPEAARFVLVTHAHMFKPTYPRSKEKLIGPSALFFHQGDYHSHIRKLVQSSFYPETIRKLIPDIEHIALSSLQSWANMPIVSTYQEMKKFAFDVGILAIFGHLESSYKEILKHNYNIVDKGYNSFPMSLPGTSYHKALMARKQLKTIVSEIICERREKRALQTDFLGHLLNEKNEKGRVLTQEQIADNIIGVLFAAQDTTASCLTWILKYLHDDQKLLEAVKAEQKAIYEENSREKKPLTWRQTRNMPLTHKVIVESLRMASIISFTFREAVVDVEYKGYLIPKGWKVMPLFRNIHHNPKYFSNPEVFDPSRFEVNPKPNTFMPFGSGVHACPGNELAKLQILIFLHHLVSNFRWEVKGGEKGIQYSPFPIPQNGLPATFRRHS L*Microarray data shows that the coding sequence was expressed in thefollowing experiments, which shows that the promoter would be useful tomodulate expression in situations similar to the following: CDNA_IDSHORT_NAME EXPT_REP_ID IS_UP 12370888 At_100uM_ABA 20000166 + 12370888At_100uM_ABA 20000169 + 12370888 At_42deg_Heat 20000171 + 12370888At_42deg_Heat 20000173 + 12370888 At_2mM_SA 20000182 + 12370888At_Open_Flower 20000264 + 12370888 At_Shoots 20000438 + 12370888At_100uM_ABA 20000453 + 12370888 At_42deg_Heat 20000457 − 12370888At_42deg_Heat 20000458 + 12370888 At_Guard_Cells 20000495 + 12370888At_10percent_PEG 20000527 + 12370888 At_Petals 20000794 + 12370888At_Far-red-induction 20001248 − 12370888 At_Far-red-enriched 20001504 +12370888 At_Far-red-enriched-adult 20001771 + 12370888At_Drought_Reproduction 20001906 + 12370888 At_Drought_Reproduction20001907 + 12370888 At_8deg_Cold 20002107 − 12370888 At_8deg_Cold20002108 − 12370888 At_8deg_Cold 20002109 − The parameters for themicroarray experiments listed above by Expt_Rep_ID and Short_Name are asfollow below: CDNA_ID SHORT_NAME EXPT_REP_ID PARAM_NAME VALUE 12370888At_100uM_ABA 20000166 Timepoint (hr) 1 12370888 At_100uM_ABA 20000166Age (day) 14 12370888 At_100uM_ABA 20000166 Treatment 100 uM ABA vs. NoTreatment 12370888 At_100uM_ABA 20000166 Organism A. thaliana 12370888At_100uM_ABA 20000166 Tissue Aerial 12370888 At_100uM_ABA 20000166 PlantLine WS 12370888 At_100uM_ABA 20000169 Timepoint (hr) 6 12370888At_100uM_ABA 20000169 Age (day) 14 12370888 At_100uM_ABA 20000169Treatment 100 uM ABA vs. No Treatment 12370888 At_100uM_ABA 20000169Organism A. thaliana 12370888 At_100uM_ABA 20000169 Tissue Aerial12370888 At_100uM_ABA 20000169 Plant Line WS 12370888 At_42deg_Heat20000171 Timepoint (hr) 1 12370888 At_42deg_Heat 20000171 Age (day) 1412370888 At_42deg_Heat 20000171 Temperature (deg C.) 42 vs. 22 12370888At_42deg_Heat 20000171 Organism A. thaliana 12370888 At_42deg_Heat20000171 Tissue Aerial 12370888 At_42deg_Heat 20000171 Plant Line WS12370888 At_42deg_Heat 20000173 Timepoint (hr) 6 12370888 At_42deg_Heat20000173 Age (day) 14 12370888 At_42deg_Heat 20000173 Temperature (degC.) 42 vs. 22 12370888 At_42deg_Heat 20000173 Organism A. thaliana12370888 At_42deg_Heat 20000173 Tissue Aerial 12370888 At_42deg_Heat20000173 Plant Line WS 12370888 At_2mM_SA 20000182 Timepoint (hr) 612370888 At_2mM_SA 20000182 Age (day) 14 12370888 At_2mM_SA 20000182Treatment 2 mM SA vs. No Treatment 12370888 At_2mM_SA 20000182 OrganismA. thaliana 12370888 At_2mM_SA 20000182 Tissue Aerial 12370888 At_2mM_SA20000182 Plant Line WS 12370888 At_Open_Flower 20000264 Age (day) 2112370888 At_Open_Flower 20000264 Organism A. thaliana 12370888At_Open_Flower 20000264 Tissue Open Flower vs. Whole Plant 12370888At_Open_Flower 20000264 Plant Line WS 12370888 At_Shoots 20000438 Age(day) 14 vs. 21 12370888 At_Shoots 20000438 Organism A. thaliana12370888 At_Shoots 20000438 Tissue Shoots vs. Whole Plant 12370888At_Shoots 20000438 Plant Line WS 12370888 At_100uM_ABA 20000453 Age(day) 15 12370888 At_100uM_ABA 20000453 Timepoint (hr) 24 12370888At_100uM_ABA 20000453 Treatment 100 uM ABA vs. No Treatment 12370888At_100uM_ABA 20000453 Organism A. thaliana 12370888 At_100uM_ABA20000453 Tissue Aerial 12370888 At_100uM_ABA 20000453 Plant Line WS12370888 At_42deg_Heat 20000457 Timepoint (hr) 0.166 12370888At_42deg_Heat 20000457 Age (day) 14 12370888 At_42deg_Heat 20000457Temperature (deg C.) 42 vs. 22 12370888 At_42deg_Heat 20000457 OrganismA. thaliana 12370888 At_42deg_Heat 20000457 Tissue Aerial 12370888At_42deg_Heat 20000457 Plant Line WS 12370888 At_42deg_Heat 20000458Timepoint (hr) 8 12370888 At_42deg_Heat 20000458 Age (day) 14 12370888At_42deg_Heat 20000458 Temperature (deg C.) 42 vs. 22 12370888At_42deg_Heat 20000458 Organism A. thaliana 12370888 At_42deg_Heat20000458 Tissue Aerial 12370888 At_42deg_Heat 20000458 Plant Line WS12370888 At_Guard_Cells 20000495 Harvest Date Aug. 02, 2002 12370888At_Guard_Cells 20000495 Organism A. thaliana 12370888 At_Guard_Cells20000495 Tissue Guard Cells vs. Leaves 12370888 At_10percent_PEG20000527 Age (day) 20 12370888 At_10percent_PEG 20000527 Timepoint (day)20 12370888 At_10percent_PEG 20000527 Treatment 10 percent PEG vs. NoTreatment 12370888 At_10percent_PEG 20000527 Organism A. thaliana12370888 At_10percent_PEG 20000527 Tissue Whole Plant 12370888At_10percent_PEG 20000527 Plant Line WS 12370888 At_Petals 20000794 Age(day) 23-25 days 12370888 At_Petals 20000794 Organism A. thaliana12370888 At_Petals 20000794 Tissue Petals vs. Whole plant 12370888At_Petals 20000794 Plant Line WS 12370888 At_Far-red-induction 20001248Timepoint (hr) 4 12370888 At_Far-red-induction 20001248 Age (day) 712370888 At_Far-red-induction 20001248 Organism A. thaliana 12370888At_Far-red-induction 20001248 Plant Line Columbia 12370888At_Far-red-induction 20001248 Light Far-red vs. White 12370888At_Far-red-induction 20001248 Tissue Whole Plant 12370888At_Far-red-enriched 20001504 Timepoint (day) 6 12370888At_Far-red-enriched 20001504 Age (day) 10 12370888 At_Far-red-enriched20001504 Organism A. thaliana 12370888 At_Far-red-enriched 20001504Plant Line Columbia 12370888 At_Far-red-enriched 20001504 Light Far-redenriched vs. White 12370888 At_Far-red-enriched 20001504 Tissue WholePlant 12370888 At_Far-red-enriched-adult 20001771 Timepoint (hr) 1612370888 At_Far-red-enriched-adult 20001771 Age (day) 28 12370888At_Far-red-enriched-adult 20001771 Organism A. thaliana 12370888At_Far-red-enriched-adult 20001771 Tissue Aerial 12370888At_Far-red-enriched-adult 20001771 Plant Line Columbia 12370888At_Far-red-enriched-adult 20001771 Light Far-red enriched vs. White12370888 At_Drought_Reproduction 20001906 Timepoint (day) 5 12370888At_Drought_Reproduction 20001906 Age (day) 35 12370888At_Drought_Reproduction 20001906 Organism A. thaliana 12370888At_Drought_Reproduction 20001906 Treatment Drought vs. No Drought12370888 At_Drought_Reproduction 20001906 Tissue Siliques 12370888At_Drought_Reproduction 20001906 Plant Line WS 12370888At_Drought_Reproduction 20001907 Timepoint (day) 7 12370888At_Drought_Reproduction 20001907 Age (day) 37 12370888At_Drought_Reproduction 20001907 Organism A. thaliana 12370888At_Drought_Reproduction 20001907 Treatment Drought vs. No Drought12370888 At_Drought_Reproduction 20001907 Tissue Siliques 12370888At_Drought_Reproduction 20001907 Plant Line WS 12370888At_Drought_Reproduction 20001910 Timepoint (day) 7 12370888At_Drought_Reproduction 20001910 Age (day) 37 12370888At_Drought_Reproduction 20001910 Organism A. thaliana 12370888At_Drought_Reproduction 20001910 Treatment Drought vs. No Drought12370888 At_Drought_Reproduction 20001910 Tissue Flowers 12370888At_Drought_Reproduction 20001910 Plant Line WS 12370888 At_8deg_Cold20002107 Age (day) 11 12370888 At_8deg_Cold 20002107 Timepoint (hr) 9612370888 At_8deg_Cold 20002107 Temperature (deg C.) 8 vs. 22 12370888At_8deg_Cold 20002107 Organism A. thaliana 12370888 At_8deg_Cold20002107 Tissue Whole Plant 12370888 At_8deg_Cold 20002107 Plant Line WS12370888 At_8deg_Cold 20002108 Age (day) 14 12370888 At_8deg_Cold20002108 Timepoint (hr) 168 12370888 At_8deg_Cold 20002108 Temperature(deg C.) 8 vs. 22 12370888 At_8deg_Cold 20002108 Organism A. thaliana12370888 At_8deg_Cold 20002108 Tissue Whole Plant 12370888 At_8deg_Cold20002108 Plant Line WS 12370888 At_8deg_Cold 20002109 Age (day) 1612370888 At_8deg_Cold 20002109 Timepoint (hr) 216 12370888 At_8deg_Cold20002109 Temperature (deg C.) 8 vs. 22 12370888 At_8deg_Cold 20002109Organism A. thaliana 12370888 At_8deg_Cold 20002109 Tissue Whole Plant12370888 At_8deg_Cold 20002109 Plant Line WS Promoter YP0371 Modulatesthe gene: Unknown protein. Contains putative conserved domains: [ATPasefamily associated with various cellular activities (AAA). AAA familyproteins often perform chaperone-like functions that assist in theassembly, operation, or disassembly of protein complexes] The GenBankdescription of the gene: NM_179511 Arabidopsis thaliana AAA-type ATPasefamily protein (At1g64110) mRNA, complete cdsgi|30696967|ref|NM_179511.1|[30696967]. The promoter sequence:5′gattctgcgaagacaggagaagccatacctttcaatctaagccgtcaacttgttcccttacgtgggatcctattatacaatccaacggttctaaatgagccacgccttccagatctaacacagtcatgctttctacagtctgcaccccttttttttttagtgttttatctacattttttcctttgtgtttaattttgtgccaacatctataacttacccctataaaaatattcaattatcacagaatacccacaatcgaaaacaaaatttaccggaataatttaattaaagctggactataatgacaattccgaaactatcaaggaataaattaaagaaactaaaaaactaaagggcattagagtaaagaagcggcaacatcagaattaaaaaactgccgaaaaaccaacctagtagccgtttatatgacaacacgtacgcaaagtctcggtaatgactcatcagttttcatgtgcaaacatattacccccatgaaataaaaaagcagagaagcgatcaaaaaaatcttcattaaaagaaccctaaatctctcatatccgccgccgtctttgcctcattttcaacaccggtgatgacgtgtaaatagatctggttttcacggttctcactactctctgtgatttttcagactattgaatcgttaggaccaaaacaagtacaaagaaactgcagaagaaaagatttgagagagatatcttacgaaacaaggtatatatttctcttgttaaatctttgaaaatactttcaaagtttcggttggattctcgaataagttaggttaaatagtcaatatagaattatagataaatcgataccttttgtttgttatcattcaatttttattgttgttacgattagtaacaacgttttagatcttgatctaTATAttaataatactaatactttgtttttttttgttttttttttaa 3′-aATG The promoter was cloned from theorganism:   Arabidopsis thaliana, Columbia ecotype Alternativenucleotides: Predicted Position (bp) Mismatch Predicted/Experimental 155PCR error or ecotype variant SNP t/c The promoter was cloned in thevector: pNewbin4-HAP1-GFP When cloned into the vector the promoter wasoperably linked to a marker, which was the type: GFP-ER Promoter-markervector was tested in: Arabidopsis thaliana, WS ecotype Generationscreened:   XT1 Mature XT2 Seedling   T2 Mature   T3 Seedling Thespatial expression of the promoter-marker vector was found observed inand would be useful in expression in any or all of the following: FlowerM pedicel M stomata Primary Root L epidermis Observed expression patternof the promoter-marker vector was in: T1 mature: Weak guard cellexpression in pedicles. T2 seedling: Weak root epidermal expression.Misc. promoter information:   Bidirectionality: Pass  Exons: Pass   Repeats: No An overlap in an exon with the endogenous coding sequenceto the promoter occurs at base pairs 537-754 The Ceres cDNA ID of theendogenous coding sequence to the promoter: 12657397 cDNA nucleotidesequence:AGCGATCAAAAAAATCTTCATTAAAAGAACCCTAAATCTCTCATATCCGCCGCCGTCTTTGCCTCATTTTCAACACCGGTGATGACGTGTAAATAGATCTGGTTTTCACGGTTCTCACTACTCTCTGTGATTTTTCAGACTATTGAATCGTTAGGACCAAAACAAGTACAAAGAAACTGCAGAAGAAAAGATTTGAGAGAGATATCTTACGAAACAAGCAAACAGATGTTGTTGTCGGCGCTTGGCGTCGGAGTTGGAGTAGGTGTGGGTTTAGGCTTGGCTTCTGGTCAAGCCGTCGGAAAATGGGCCGGCGGGAACTCGTCGTCAAATAACGCCGTCACGGCGGATAAGATGGAGAAGGAGATACTCCGTCAAGTTGTTGACGGCAGAGAGAGTAAAATTACTTTCGATGAGTTTCCTTATTATCTCAGTGAACAAACACGAGTGCTTCTAACAAGTGCAGCTTATGTCCATTTGAAGCACTTCGATGCTTCAAAATATACGAGAAACTTGTCTCCAGCTAGCCGAGCCATTCTCTTGTCCGGCCCTGCCGAGCTTTACCAACAAATGCTAGCCAAAGCCCTAGCTCATTTCTTCGATGCCAAGTTACTTCTTCTAGACGTCAACGATTTTGCACTCAAGATACAGAGCAAATACGGCAGTGGAAATACAGAATCATCGTCATTCAAGAGATCTCCCTCAGAATCTGCTTTAGAGCAACTATCAGGACTGTTTAGTTCCTTCTCCATCCTTCCTCAGAGAGAAGAGTCAAAAGCTGGTGGTACCTTGAGGAGGCAAAGCAGTGGTGTGGATATCAAATCAAGCTCAATGGAAGGCTCTAGTAATCCTCCAAAGCTTCGTCGAAACTCTTCAGCAGCAGCTAATATTAGCAACCTTGCATCTTCCTCAAATCAAGTTTCAGCGCCTTTGAAACGAAGTAGCAGTTGGTCATTCGATGAAAAGCTTCTCGTCCAATCTTTATATAAGGTCTTGGCCTATGTCTCCAAGGCGAATCCGATTGTGTTATATCTTCGAGACGTCGAGAACTTTCTGTTCCGCTCACAGAGAACTTACAACTTGTTCCAGAAGCTTCTCCAGAAACTCAGTGGACCGGTCCTCATTCTCGGTTCAAGAATTGTGGACTTGTCAAGCGAAGACGCTCAAGAAATTGATGAGAAGCTCTCTGCTGTTTTCCCTTATAATATCGACATAAGACCTCCTGAGGATGAGACTCATCTAGTGAGCTGGAAATCGCAGCTTGAACGCGACATGAACATGATCCAAACTCAGGACAATAGGAACCATATCATGGAAGTTTTGTCGGAGAATGATCTTATATGCGATGACCTTGAATCCATCTCTTTTGAGGACACGAAGGTTTTAAGCAATTACATTGAAGAGATCGTTGTCTCTGCTCTTTCCTATCATCTGATGAACAACAAAGATCCTGAGTACAGAAACGGAAAACTGGTGATATCTTCTATAAGTTTGTCGCATGGATTCAGTCTCTTCAGAGAAGGCAAAGCTGGCGGTCGTGAGAAGCTGAAGCAAAAAACTAAGGAGGAATCATCCAAGGAAGTAAAAGCTGAATCAATCAAGCCGGAGACAAAAACAGAGAGTGTCACCACCGTAAGCAGCAAGGAAGAACCAGAGAAAGAAGCTAAAGCTGAGAAAGTTACCCCAAAAGCTCCGGAAGTTGCACCGGATAACGAGTTTGAGAAACGGATAAGACCGGAAGTAATCCCAGCAGAAGAAATTAACGTCACATTCAAAGACATTGGTGCACTTGACGAGATAAAAGAGTCACTACAAGAACTTGTAATGCTTCCTCTCCGTAGGCCAGACCTCTTCACAGGAGGTCTCTTGAAGCCCTGCAGAGGAATCTTACTCTTCGGTCCACCGGGTACAGGTAAAACAATGCTAGCTAAAGCCATTGCCAAAGAGGCAGGAGCGAGTTTCATAAACGTTTCGATGTCAACAATAACTTCGAAATGGTTTGGAGAAGACGAGAAGAATGTTAGGGCTTTGTTTACTCTAGCTTCGAAGGTGTCACCAACCATAATATTTGTGGATGAAGTTGATAGTATGTTGGGACAGAGAACAAGAGTTGGAGAACATGAAGCTATGAGAAAGATCAAGAATGAGTTTATGAGTCATTGGGATGGGTTAATGACTAAACCTGGTGAACGTATCTTAGTCCTTGCTGCTACTAATCGGCCTTTCGATCTTGATGAAGCCATTATCAGACGATTCGAACGAAGGATCATGGTGGGACTACCGGCTGTAGAGAACAGAGAAAAGATTCTAAGAACATTGTTGGCGAAGGAGAAAGTAGATGAAAACTTGGATTACAAGGAACTAGCAATGATGACAGAAGGATACACAGGAAGTGATCTTAAGAATCTGTGCACAACCGCTGCGTATAGGCCGGTGAGAGAACTTATACAGCAAGAGAGGATCAAAGACACAGAGAAGAAGAAGCAGAGAGAGCCTACAAAAGCAGGTGAAGAAGATGAAGGAAAAGAAGAGAGAGTTATAACACTTCGTCCGTTGAACAGACAAGACTTTAAAGAAGCCAAGAATCAGGTGGCGGCGAGTTTTGCGGCTGAGGGAGCGGGAATGGGAGAGTTGAAGCAGTGGAATGAATTGTATGGAGAAGGAGGATCGAGGAAGAAAGAACAACTCACTTACTTCTTGTAATGATGATGATGAATCATGATGCTGGTAATGGATTATGAAATTTGGTAATGTAATAGTATGGTGAATTTTTGTTTCCATGGTTAATAAGAGAATAAGAATATGATGATATTGCTAAAAGTTTGACCCGT Codingsequence:MLLSALGVGVGVGVGLGLASGQAVGKWAGGNSSSNNAVTADKMEKEILRQVVDGRESKITFDEFPYYLSEQTRVLLTSAAYVHLKHFDASKYTRNLSPASRAILLSGPAELYQQMLAKALAHFFDAKLLLLDVNDFALKIQSKYGSGNTESSSFKRSPSESALEQLSGLFSSFSILPQREESKAGGTLRRQSSGVDIKSSSMEGSSNPPKLRRNSSAAANISNLASSSNQVSAPLKRSSSWSFDEKLLVQSLYKVLAYVSKANPIVLYLRDVENFLFRSQRTYNLFQKLLQKLSGPVLILGSRIVDLSSEDAQEIDEKLSAVFPYNIDIRPPEDETHLVSWKSQLERDMNMIQTQDNRNHIMEVLSENDLICDDLESISFEDTKVLSNYIEEIVVSALSYHLMNNKDPEYRNGKLVISSISLSHGFSLFREGKAGGREKLKQKTKEESSKEVKAESIKPETKTESVTTVSSKEEPEKEAKAEKVTPKAPEVAPDNEFEKRIRPEVIPAEEINVTFKDIGALDEIKESLQELVMLPLRRPDLFTGGLLKPCRGILLFGPPGTGKTMLAKAIAKEAGASFINVSMSTITSKWFGEDEKNVRALFTLASKVSPTIIFVDEVDSMLGQRTRVGEHEAMRKIKNEFMSHWDGLMTKPGERILVLAATNRPFDLDEAIIRRFERRIMVGLPAVENREKILRTLLAKEKVDENLDYKELAMMTEGYTGSDLKNLCTTAAYRPVRELIQQERIKDTEKKKQREPTKAGEEDEGKEERVITLRPLNRQDFKEAKNQVAASFAAEGAGMGELKQWNELYGEGGSRKKEQLTYFL* Microarray data shows that the coding sequencewas expressed in the following experiments, which shows that thepromoter would be useful to modulate expression in situations similar tothe following: CDNA_ID SHORT_NAME EXPT_REP_ID IS_UP 12657397At_100uM_ABA 20000169 + 12657397 At_Germinating_Seeds 20000180 −12657397 At_Roots 20000185 + 12657397 At_Siliques 20000234 − 12657397At_Siliques 20000235 − 12657397 At_Siliques 20000236 − 12657397At_Drought 20000267 + 12657397 At_100mM_NaCl 20000268 + 12657397At_100mM_NaCl 20000308 + 12657397 At_Pollen 20000326 + 12657397At_Drought 20000436 + 12657397 At_Drought 20000437 + 12657397 At_Roots20000439 + 12657397 At_10percent_PEG 20000460 + 12657397At_10percent_PEG 20000527 + 12657397 At_100uM_ABA_Mutants 20000575 +12657397 At_100uM_ABA_Mutants 20000576 + 12657397 At_Herbicide_Mutants20000639 + 12657397 At_Herbicide_Mutants 20000642 + 12657397At_Line_Comparisons 20001300 − 12657397 At_Line_Comparisons 20001307 +12657397 At_Line_Comparisons 20001309 − 12657397 At_Line_Comparisons20001310 − 12657397 At_Line_Comparisons 20001319 + 12657397At_Far-red-induction 20001451 + 12657397 At_Far-red-enriched 20001504 +12657397 At_Drought_Soil_Dry 20001554 + 12657397 At_Drought_Soil_Dry20001555 + 12657397 At_Drought_Soil_Dry 20001556 + 12657397At_Drought_Soil_Dry 20001557 + 12657397 At_Drought_Soil_Dry 20001559 +12657397 At_Drought_Soil_Dry 20001560 + 12657397 At_Drought_Reproduction20001904 + 12657397 At_Drought_Reproduction 20001906 + 12657397At_Drought_Reproduction 20001907 + 12657397 At_Drought_Reproduction20001909 + 12657397 At_Line_Comparisons 20002009 + 12657397At_Drought-Air-Dry 20002256 + The parameters for the microarrayexperiments listed above by Expt_Rep_ID and Short_Name are as followbelow: CDNA_ID SHORT_NAME EXPT_REP_ID PARAM_NAME VALUE 12657397At_100uM_ABA 20000169 Timepoint (hr) 6 12657397 At_100uM_ABA 20000169Age (day) 14 12657397 At_100uM_ABA 20000169 Treatment 100 uM ABA vs. NoTreatment 12657397 At_100uM_ABA 20000169 Organism A. thaliana 12657397At_100uM_ABA 20000169 Tissue Aerial 12657397 At_100uM_ABA 20000169 PlantLine WS 12657397 At_Germinating_Seeds 20000180 Age (hr) 24 vs. 012657397 At_Germinating_Seeds 20000180 Organism A. thaliana 12657397At_Germinating_Seeds 20000180 Tissue Germinating Seeds 12657397At_Germinating_Seeds 20000180 Plant Line WS 12657397 At_Roots 20000185Age (day) 7 vs. 21 12657397 At_Roots 20000185 Organism A. thaliana12657397 At_Roots 20000185 Tissue Roots vs. Whole Plant 12657397At_Roots 20000185 Plant Line WS 12657397 At_Siliques 20000234 Age (day)21 12657397 At_Siliques 20000234 Tissue <5 mm Siliques vs. Whole Plant12657397 At_Siliques 20000234 Organism A. thaliana 12657397 At_Siliques20000234 Plant Line WS 12657397 At_Siliques 20000235 Age (day) 2112657397 At_Siliques 20000235 Tissue 5-10 mm Siliques vs. Whole Plant12657397 At_Siliques 20000235 Organism A. thaliana 12657397 At_Siliques20000235 Plant Line WS 12657397 At_Siliques 20000236 Age (day) 2112657397 At_Siliques 20000236 Tissue >10 mm Siliques vs. Whole Plant12657397 At_Siliques 20000236 Organism A. thaliana 12657397 At_Siliques20000236 Plant Line WS 12657397 At_Drought 20000267 Timepoint (hr) 612657397 At_Drought 20000267 Age (day) 7 12657397 At_Drought 20000267Organism A. thaliana 12657397 At_Drought 20000267 Treatment Drought vs.No Drought 12657397 At_Drought 20000267 Tissue Whole Plant 12657397At_Drought 20000267 Plant Line WS 12657397 At_100mM_NaCl 20000268Timepoint (hr) 6 12657397 At_100mM_NaCl 20000268 Age (day) 14 12657397At_100mM_NaCl 20000268 Treatment 100 mM NaCl vs. No Treatment 12657397At_100mM_NaCl 20000268 Organism A. thaliana 12657397 At_100mM_NaCl20000268 Tissue Whole Plant 12657397 At_100mM_NaCl 20000268 Plant LineWS 12657397 At_100mM_NaCl 20000308 Age (day) 17 12657397 At_100mM_NaCl20000308 Timepoint (hr) 72 12657397 At_100mM_NaCl 20000308 Treatment 100mM NaCl vs. No Treatment 12657397 At_100mM_NaCl 20000308 Organism A.thaliana 12657397 At_100mM_NaCl 20000308 Tissue Whole Plant 12657397At_100mM_NaCl 20000308 Plant Line WS 12657397 At_Pollen 20000326 Age(day) 0 vs. 21 12657397 At_Pollen 20000326 Organism A. thaliana 12657397At_Pollen 20000326 Tissue Pollen vs. Whole Plant 12657397 At_Pollen20000326 Plant Line WS 12657397 At_Drought 20000436 Age (day) 7 12657397At_Drought 20000436 Timepoint (hr) 12 12657397 At_Drought 20000436Organism A. thaliana 12657397 At_Drought 20000436 Treatment Drought vs.No Drought 12657397 At_Drought 20000436 Tissue Whole Plant 12657397At_Drought 20000436 Plant Line WS 12657397 At_Drought 20000437 Age (day)8 12657397 At_Drought 20000437 Timepoint (hr) 24 12657397 At_Drought20000437 Organism A. thaliana 12657397 At_Drought 20000437 TreatmentDrought vs. No Drought 12657397 At_Drought 20000437 Tissue Whole Plant12657397 At_Drought 20000437 Plant Line WS 12657397 At_Roots 20000439Age (day) 14 vs. 21 12657397 At_Roots 20000439 Organism A. thaliana12657397 At_Roots 20000439 Tissue Roots vs. Whole Plant 12657397At_Roots 20000439 Plant Line WS 12657397 At_10percent_PEG 20000460 Age(day) 12 12657397 At_10percent_PEG 20000460 Timepoint (day) 12 12657397At_10percent_PEG 20000460 Treatment 10 percent PEG vs. No Treatment12657397 At_10percent_PEG 20000460 Organism A. thaliana 12657397At_10percent_PEG 20000460 Tissue Whole Plant 12657397 At_10percent_PEG20000460 Plant Line WS 12657397 At_10percent_PEG 20000527 Age (day) 2012657397 At_10percent_PEG 20000527 Timepoint (day) 20 12657397At_10percent_PEG 20000527 Treatment 10 percent PEG vs. No Treatment12657397 At_10percent_PEG 20000527 Organism A. thaliana 12657397At_10percent_PEG 20000527 Tissue Whole Plant 12657397 At_10percent_PEG20000527 Plant Line WS 12657397 At_100uM_ABA_Mutants 20000575 Timepoint(hr) 6 12657397 At_100uM_ABA_Mutants 20000575 Treatment 1 uM ABA vs. NoTreatment 12657397 At_100uM_ABA_Mutants 20000575 Organism A. thaliana12657397 At_100uM_ABA_Mutants 20000575 Plant Line CS22 12657397At_100uM_ABA_Mutants 20000575 Tissue Whole Plant 12657397At_100uM_ABA_Mutants 20000576 Timepoint (hr) 6 12657397At_100uM_ABA_Mutants 20000576 Treatment 1 uM ABA vs. No Treatment12657397 At_100uM_ABA_Mutants 20000576 Organism A. thaliana 12657397At_100uM_ABA_Mutants 20000576 Plant Line CS23 12657397At_100uM_ABA_Mutants 20000576 Tissue Whole Plant 12657397At_Herbicide_Mutants 20000639 Timepoint (hr) 4 12657397At_Herbicide_Mutants 20000639 Plant Line 05377RR/BR27173 12657397At_Herbicide_Mutants 20000639 Treatment Roundup vs. No Treatment12657397 At_Herbicide_Mutants 20000639 Tissue Seedlings 12657397At_Herbicide_Mutants 20000642 Timepoint (hr) 12 12657397At_Herbicide_Mutants 20000642 Plant Line 3950BR/PCJE10000 12657397At_Herbicide_Mutants 20000642 Treatment Finale vs. No Treatment 12657397At_Herbicide_Mutants 20000642 Tissue Seedlings 12657397At_Line_Comparisons 20001300 Plant Line ME01338-05 vs. WS 12657397At_Line_Comparisons 20001307 Plant Line WBin4-WX2-A vs. WS 12657397At_Line_Comparisons 20001309 Plant Line WBin4-WX49R-A vs. WS 12657397At_Line_Comparisons 20001310 Plant Line WBin4-WX17-A vs. WS 12657397At_Line_Comparisons 20001319 Plant Line WBin4-WX24-A vs. WS 12657397At_Far-red-induction 20001451 Age (day) 8 12657397 At_Far-red-induction20001451 Timepoint (hr) 24 12657397 At_Far-red-induction 20001451Organism A. thaliana 12657397 At_Far-red-induction 20001451 Plant LineColumbia 12657397 At_Far-red-induction 20001451 Light Far-red vs. White12657397 At_Far-red-induction 20001451 Tissue Whole Plant 12657397At_Far-red-enriched 20001504 Timepoint (day) 6 12657397At_Far-red-enriched 20001504 Age (day) 10 12657397 At_Far-red-enriched20001504 Organism A. thaliana 12657397 At_Far-red-enriched 20001504Plant Line Columbia 12657397 At_Far-red-enriched 20001504 Light Far-redenriched vs. White 12657397 At_Far-red-enriched 20001504 Tissue WholePlant 12657397 At_Drought_Soil_Dry 20001554 Timepoint (day) 7 12657397At_Drought_Soil_Dry 20001554 Age (day) 21 12657397 At_Drought_Soil_Dry20001554 Organism A. thaliana 12657397 At_Drought_Soil_Dry 20001554Treatment Drought vs. No Drought 12657397 At_Drought_Soil_Dry 20001554Post Timepoint (hr) None 12657397 At_Drought_Soil_Dry 20001554Post-Treatment None 12657397 At_Drought_Soil_Dry 20001554 Plant Line WS12657397 At_Drought_Soil_Dry 20001555 Timepoint (day) 10 12657397At_Drought_Soil_Dry 20001555 Age (day) 24 12657397 At_Drought_Soil_Dry20001555 Organism A. thaliana 12657397 At_Drought_Soil_Dry 20001555Treatment Drought vs. No Drought 12657397 At_Drought_Soil_Dry 20001555Post Timepoint (hr) None 12657397 At_Drought_Soil_Dry 20001555Post-Treatment None 12657397 At_Drought_Soil_Dry 20001555 Plant Line WS12657397 At_Drought_Soil_Dry 20001556 Timepoint (day) 12 12657397At_Drought_Soil_Dry 20001556 Age (day) 26 12657397 At_Drought_Soil_Dry20001556 Organism A. thaliana 12657397 At_Drought_Soil_Dry 20001556Treatment Drought vs. No Drought 12657397 At_Drought_Soil_Dry 20001556Post Timepoint (hr) None 12657397 At_Drought_Soil_Dry 20001556Post-Treatment None 12657397 At_Drought_Soil_Dry 20001556 Plant Line WS12657397 At_Drought_Soil_Dry 20001557 Post Timepoint (hr) 3 12657397At_Drought_Soil_Dry 20001557 Timepoint (day) 13 12657397At_Drought_Soil_Dry 20001557 Age (day) 27 12657397 At_Drought_Soil_Dry20001557 Organism A. thaliana 12657397 At_Drought_Soil_Dry 20001557Treatment Drought vs. No Drought 12657397 At_Drought_Soil_Dry 20001557Post-Treatment Re-Water vs. No Drought 12657397 At_Drought_Soil_Dry20001557 Plant Line WS 12657397 At_Drought_Soil_Dry 20001559 Timepoint(day) 14 12657397 At_Drought_Soil_Dry 20001559 Age (day) 28 12657397At_Drought_Soil_Dry 20001559 Post Timepoint (hr) 29 12657397At_Drought_Soil_Dry 20001559 Organism A. thaliana 12657397At_Drought_Soil_Dry 20001559 Treatment Drought vs. No Drought 12657397At_Drought_Soil_Dry 20001559 Post-Treatment Re-Water vs. No Drought12657397 At_Drought_Soil_Dry 20001559 Plant Line WS 12657397At_Drought_Soil_Dry 20001560 Timepoint (day) 14 12657397At_Drought_Soil_Dry 20001560 Age (day) 28 12657397 At_Drought_Soil_Dry20001560 Organism A. thaliana 12657397 At_Drought_Soil_Dry 20001560Treatment Drought vs. No Drought 12657397 At_Drought_Soil_Dry 20001560Post Timepoint (hr) None 12657397 At_Drought_Soil_Dry 20001560Post-Treatment None 12657397 At_Drought_Soil_Dry 20001560 Plant Line WS12657397 At_Drought_Reproduction 20001904 Timepoint (day) 7 12657397At_Drought_Reproduction 20001904 Age (day) 37 12657397At_Drought_Reproduction 20001904 Organism A. thaliana 12657397At_Drought_Reproduction 20001904 Treatment Drought vs. No Drought12657397 At_Drought_Reproduction 20001904 Tissue Rosettes 12657397At_Drought_Reproduction 20001904 Plant Line WS 12657397At_Drought_Reproduction 20001906 Timepoint (day) 5 12657397At_Drought_Reproduction 20001906 Age (day) 35 12657397At_Drought_Reproduction 20001906 Organism A. thaliana 12657397At_Drought_Reproduction 20001906 Treatment Drought vs. No Drought12657397 At_Drought_Reproduction 20001906 Tissue Siliques 12657397At_Drought_Reproduction 20001906 Plant Line WS 12657397At_Drought_Reproduction 20001907 Timepoint (day) 7 12657397At_Drought_Reproduction 20001907 Age (day) 37 12657397At_Drought_Reproduction 20001907 Organism A. thaliana 12657397At_Drought_Reproduction 20001907 Treatment Drought vs. No Drought12657397 At_Drought_Reproduction 20001907 Tissue Siliques 12657397At_Drought_Reproduction 20001907 Plant Line WS 12657397At_Drought_Reproduction 20001909 Timepoint (day) 5 12657397At_Drought_Reproduction 20001909 Age (day) 35 12657397At_Drought_Reproduction 20001909 Organism A. thaliana 12657397At_Drought_Reproduction 20001909 Treatment Drought vs. No Drought12657397 At_Drought_Reproduction 20001909 Tissue Flowers 12657397At_Drought_Reproduction 20001909 Plant Line WS 12657397At_Line_Comparisons 20002009 Plant Line ME01642 vs. WS 12657397At_Drought-Air-Dry 20002256 Timepoint (hr) 4 12657397 At_Drought-Air-Dry20002256 Age (day) 35 12657397 At_Drought-Air-Dry 20002256 Organism A.thaliana 12657397 At_Drought-Air-Dry 20002256 Treatment Drought vs. NoDrought 12657397 At_Drought-Air-Dry 20002256 Tissue Shoots 12657397At_Drought-Air-Dry 20002256 Plant Line WS Promoter YP0356 Modulates thegene: Dehydration-induced protein RD22 The GenBank description of thegeneNM_122472 Arabidopsis thaliana dehydration-induced protein RD22(At5g25610) mRNA, complete cds gi|30689960|ref|NM_122472.2|[30689960]The promoter sequence:5′tacttgcaaccactttgtaggaccattaactgcaaaataagaattctctaagcttcacaaggggttcgtttggtgctataaaaacattgttttaagaactggtttactggttctataaatctataaatccaaatatgaagtatggcaataataataacatgttagcacaaaaaatactcattaaattcctacccaaaaaaaatctttatatgaaactaaaacttatatacacaataatagtgatacaaagtaggtcttgatattcaactattcgggattttctggtttcgagtaattcgtataaaaggtttaagatctattatgttcactgaaatcttaactttgttttgtttccagttttaactagtagaaattgaaagttttaaaaattgttacttacaataaaatttgaatcaatatccttaatcaaaggatcttaagactagcacaattaaaacatataacgtagaatatctgaaataactcgaaaatatctgaactaagttagtagttttaaaatataatcccggtttggaccgggcagtatgtacttcaatacttgtgggttttgacgattttggatcggattgggcgggccagccagattgatctattacaaatttcacctgtcaacgctaactccgaacttaatcaaagattttgagctaaggaaaactaatcagtgatcacccaaagaaaacattcgtgaataattgtttgctttccatggcagcaaaacaaataggacccaaataggaatgtcaaaaaaaagaaagacacgaaacgaagtagtataacgtaacacacaaaaataaactagagatattaaaaacacatgtccacacatggatacaagagcatttaaggagcagaaggcacgtagtggttagaaggtatgtgatataattaatcggcccaaatagattggtaagtagtagccgtcTATAtca 3′-cagctcctttctactaaaacccttttactataaattctacgtacacgtaccacttcttctcctcaaattcaThe promoter was cloned from the organism: Arabidopsis thaliana, WSecotype Alternative nucleotides: Predicted (Columbia) Experimental(Wassilewskija) Predicted Position (bp) Mismatch Columbia/Wassilewskija405 SNP g/t The promoter was cloned in the vector: pNewbin4-HAP1-GFPWhen cloned into the vector the promoter was operably linked to amarker, which was the type: GFP-ER Promoter-marker vector was testedin: Arabidopsis thaliana, WS ecotype Generation screened: XT1 Mature XT2Seedling T2 Mature T3 Seedling The spatial expression of thepromoter-marker vector was found observed in and would be useful inexpression in any or all of the following: Flower H pedicel H petal Hepidermis Silique H stigma L style L carpel L septum Lepidermis Ovule Houter integument Stem H epidermis H stomata Hypocotyl H epidermisCotyledon H epidermis Rosette Leaf H epidermis H trichome Observedexpression pattern of the promoter-marker vector was in: T1 mature: GFPexpression specific to epidermal call types. High GFP expression inepidermis of stem decreasing toward pedicles and inflorescence apex. Inthe flower, high expression observed in epidermal cells of petals andstigma, and lower expression in carpels. High expression in outerinteguments of matureing ovules. High expression throughout epidermalcells of mature lower stem. T2 seedling: GFP expression specific toepidermal cell types. High expression in epidermis of hypocotyl,cotyledon, and trichomes of rosette leaves. Not detected in root. Misc.promoter information: Bidirectionality: Pass Exons: Pass   Repeats:None: The Ceres cDNA ID of the endogenous coding sequence to thepromoter: 12394809 cDNA nucleotide sequence:agCTCCTTTCTACTAAAACCCTTTTACTATAAATTCTACGTACACGTACCACTTCTTCTCCTCAAATTCATCAAACCCATTTCTATTCCAACTCCCAAAAATGGCGATTCGTCTTCCTCTGATCTGTCTTCTTGGTTCATTCATGGTAGTGGCGATTGCGGCTGATTTAACACCGGAGCGTTATTGGAGCACTGCTTTACCAAACACTCCCATTCCCAACTCTCTCCATAATCTTTTGACTTTCGATTTTACCGACGAGAAAAGTACCAACGTCCAAGTAGGTAAAGGCGGAGTAAACGTTAACACCCATAAAGGTAAAACCGGTAGCGGAACCGCCGTGAACGTTGGAAAGGGAGGTGTACGCGTGGACACAGGCAAGGGCAAGCCCGGAGGAGGGACACACGTGAGCGTTGGCAGCGGAAAAGGTCACGGAGGTGGCGTCGCAGTCCACACGGGTAAACCCGGTAAAAGAACCGACGTAGGAGTCGGTAAAGGCGGTGTGACGGTGCACACGCGCCACAAGGGAAGACCGATTTACGTTGGTGTGAAACCAGGAGCAAACCCTTTCGTGTATAACTATGCAGCGAAGGAGACTCAGCTCCACGACGATCCTAACGCGGCTCTCTTCTTCTTGGAGAAGGACTTGGTTCGCGGGAAAGAAATGAATGTCCGGTTTAACGCTGAGGATGGTTACGGAGGCAAAACTGCGTTCTTGCCACGTGGAGAGGCTGAAACGGTGCCTTTTGGATCGGAGAAGTTTTCGGAGACGTTGAAACGTTTCTCGGTGGAAGCTGGTTCGGAAGAAGCGGAGATGATGAAGAAGACCATTGAGGAGTGTGAAGCCAGAAAAGTTAGTGGAGAGGAGAAGTATTGTGCGACGTCTTTGGAGTCGATGGTCGACTTTAGTGTTTCGAAACTTGGTAAATATCACGTCAGGGCTGTTTCCACTGAGGTGGCTAAGAAGAACGCACCGATGCAGAAGTACAAAATCGCGGCGGCTGGGGTAAAGAAGTTGTCTGACGATAAATCTGTGGTGTGTCACAAACAGAAGTACCCATTCGCGGTGTTCTACTGCCACAAGGCGATGATGACGACCGTCTACGCGGTTCCGCTCGAGGGAGAGAACGGGATGCGAGCTAAAGCAGTTGCGGTATGCCACAAGAACACCTCAGCTTGGAACCCAAACCACTTGGCCTTCAAAGTCTTAAAGGTGAAGCCAGGGACCGTTCCGGTCTGCCACTTCCTCCCGGAGACTCATGTTGTGTGGTTCAGCTACTAGATAGATCTGTTTTCTATCTTATTGTGGGTTATGTATAATTACGTTTCAGATAATCTATCTTTTGGGATGTTTTGGTTATGAATATACATACATATACATATAGTAATGCGTGGTTTCCATATAAGAGTGAAGGCATCTATATGTTTTTTTTTTTATTAACCTACGTAGCTGTCTTTTGTGGTCTGTATCTTGTGGTTTTGCAAAAACCTATAATAAAATTAGAGCTGAAATGTTACCATTTC Coding sequence: <MAIRLPLICLLGSFMVVAIA>ADLTPERYWSTALPNTPIPNSLHNLLTFDFTDEKSTNVQVGKGGVNVNTHKGKTGSGTAVNVGKGGVRVDTGKGKPGGGTHVSVGSGKGHGGGVAVHTGKPGKRTDVGVGKGGVTVHTRHKGRPIYVGVKPGANPFVYNYAAKETQLHDDPNAALFFLEKDLVRGKEMNVRFNAEDGYGGKTAFLPRGEAETVPFGSEKFSETLKRFSVEAGSEEAEMMKKTIEECEARKVSGEEKYCATSLESMVDFSVSKLGKYHVRAVSTEVAKKNAPMQKYKIAAAGVKKLSDDKSVVCHKQKYPFAVFYCHKAMMTTVYAVPLEGENGMRAKAVAVCHKNTSAWNPNHLAFKVLKVKPGTVPVCHFLPETHVVWFSY* Microarray datashows that the coding sequence was expressed in the followingexperiments, which shows that the promoter would be useful to modulateexpression in situations similar to the following: CDNA_ID SHORT_NAMEEXPT_REP_ID IS_UP 12394809 At_100 uM_ABA_Mutants 20000071 + 12394809At_100 uM_ABA 20000169 + 12394809 At_Roots 20000185 − 12394809At_Drought 20000267 + 12394809 At_100mM_NaCl 20000268 + 12394809At_Pollen 20000326 − 12394809 At_Drought 20000436 + 12394809 At_Drought20000437 + 12394809 At_Roots 20000439 − 12394809 At_100 uM_ABA20000453 + 12394809 At_100 uM_ABA_Mutants 20000573 − 12394809 At_100uM_ABA_Mutants 20000574 − 12394809 At_Far-red-induction 20001247 +12394809 At_Far-red-induction 20001248 − 12394809 At_Line_Comparisons20001310 − 12394809 At_Interploidy_Crosses 20001316 − 12394809At_Far-red-induction 20001450 − 12394809 At_Far-red-induction 20001451 −12394809 At_Drought_Soil_Dry 20001554 + 12394809 At_Drought_Soil_Dry20001555 + 12394809 At_Drought_Soil_Dry 20001556 + 12394809At_Drought_Soil_Dry 20001559 + 12394809 At_Interploidy_Crosses20001853 + 12394809 At_Drought_Reproduction 20001904 + 12394809At_Drought_Reproduction 20001911 + 12394809 At_8deg_Cold 20002107 + Theparameters for the microarray experiments listed above by Expt_Rep_IDand Short_Name are as follow below: CDNA_ID SHORT_NAME EXPT_REP_IDPARAM_NAME VALUE 12394809 At_100 uM_ABA_Mutants 20000071 Timepoint (hr)6 12394809 At_100 uM_ABA_Mutants 20000071 Treatment 100 uM ABA vs. NoTreatment 12394809 At_100 uM_ABA_Mutants 20000071 Tissue Aerial 12394809At_100 uM_ABA_Mutants 20000071 Plant Line CS8104 12394809 At_100 uM_ABA20000169 Timepoint (hr) 6 12394809 At_100 uM_ABA 20000169 Age (day) 1412394809 At_100 uM_ABA 20000169 Treatment 100 uM ABA vs. No Treatment12394809 At_100 uM_ABA 20000169 Organism A. thaliana 12394809 At_100uM_ABA 20000169 Tissue Aerial 12394809 At_100 uM_ABA 20000169 Plant LineWS 12394809 At_Roots 20000185 Age (day) 7 vs. 21 12394809 At_Roots20000185 Organism A. thaliana 12394809 At_Roots 20000185 Tissue Rootsvs. Whole Plant 12394809 At_Roots 20000185 Plant Line WS 12394809At_Drought 20000267 Timepoint (hr) 6 12394809 At_Drought 20000267 Age(day) 7 12394809 At_Drought 20000267 Organism A. thaliana 12394809At_Drought 20000267 Treatment Drought vs. No Drought 12394809 At_Drought20000267 Tissue Whole Plant 12394809 At_Drought 20000267 Plant Line WS12394809 At_100mM_NaCl 20000268 Timepoint (hr) 6 12394809 At_100mM_NaCl20000268 Age (day) 14 12394809 At_100mM_NaCl 20000268 Treatment 100 mMNaCl vs. No Treatment 12394809 At_100mM_NaCl 20000268 Organism A.thaliana 12394809 At_100mM_NaCl 20000268 Tissue Whole Plant 12394809At_100mM_NaCl 20000268 Plant Line WS 12394809 At_Pollen 20000326 Age(day) 0 vs. 21 12394809 At_Pollen 20000326 Organism A. thaliana 12394809At_Pollen 20000326 Tissue Pollen vs. Whole Plant 12394809 At_Pollen20000326 Plant Line WS 12394809 At_Drought 20000436 Age (day) 7 12394809At_Drought 20000436 Timepoint (hr) 12 12394809 At_Drought 20000436Organism A. thaliana 12394809 At_Drought 20000436 Treatment Drought vs.No Drought 12394809 At_Drought 20000436 Tissue Whole Plant 12394809At_Drought 20000436 Plant Line WS 12394809 At_Drought 20000437 Age (day)8 12394809 At_Drought 20000437 Timepoint (hr) 24 12394809 At_Drought20000437 Organism A. thaliana 12394809 At_Drought 20000437 TreatmentDrought vs. No Drought 12394809 At_Drought 20000437 Tissue Whole Plant12394809 At_Drought 20000437 Plant Line WS 12394809 At_Roots 20000439Age (day) 14 vs. 21 12394809 At_Roots 20000439 Organism A. thaliana12394809 At_Roots 20000439 Tissue Roots vs. Whole Plant 12394809At_Roots 20000439 Plant Line WS 12394809 At_100 uM_ABA 20000453 Age(day) 15 12394809 At_100 uM_ABA 20000453 Timepoint (hr) 24 12394809At_100 uM_ABA 20000453 Treatment 100 uM ABA vs. No Treatment 12394809At_100 uM_ABA 20000453 Organism A. thaliana 12394809 At_100 uM_ABA20000453 Tissue Aerial 12394809 At_100 uM_ABA 20000453 Plant Line WS12394809 At_100 uM_ABA_Mutants 20000573 Organism A. thaliana 12394809At_100 uM_ABA_Mutants 20000573 Plant Line CS22 vs. Ler wt 12394809At_100 uM_ABA_Mutants 20000573 Timepoint (hr) N/A 12394809 At_100uM_ABA_Mutants 20000573 Treatment None 12394809 At_100 uM_ABA_Mutants20000573 Tissue Whole Plant 12394809 At_100 uM_ABA_Mutants 20000574Organism A. thaliana 12394809 At_100 uM_ABA_Mutants 20000574 Plant LineCS23 vs. Ler wt 12394809 At_100 uM_ABA_Mutants 20000574 Timepoint (hr)N/A 12394809 At_100 uM_ABA_Mutants 20000574 Treatment None 12394809At_100 uM_ABA_Mutants 20000574 Tissue Whole Plant 12394809At_Far-red-induction 20001247 Timepoint (hr) 1 12394809At_Far-red-induction 20001247 Age (day) 7 12394809 At_Far-red-induction20001247 Organism A. thaliana 12394809 At_Far-red-induction 20001247Plant Line Columbia 12394809 At_Far-red-induction 20001247 Light Far-redvs. White 12394809 At_Far-red-induction 20001247 Tissue Whole Plant12394809 At_Far-red-induction 20001248 Timepoint (hr) 4 12394809At_Far-red-induction 20001248 Age (day) 7 12394809 At_Far-red-induction20001248 Organism A. thaliana 12394809 At_Far-red-induction 20001248Plant Line Columbia 12394809 At_Far-red-induction 20001248 Light Far-redvs. White 12394809 At_Far-red-induction 20001248 Tissue Whole Plant12394809 At_Line_Comparisons 20001310 Plant Line WBin4-WX17-A vs. WS12394809 At_Interploidy_Crosses 20001316 Age (day) 5 12394809At_Interploidy_Crosses 20001316 Organism A. thaliana 12394809At_Interploidy_Crosses 20001316 Plant Line Columbia 12394809At_Interploidy_Crosses 20001316 Cross hemi × 2X vs. 2X × 2X 12394809At_Interploidy_Crosses 20001316 Tissue Siliques 12394809At_Far-red-induction 20001450 Age (day) 7 12394809 At_Far-red-induction20001450 Timepoint (hr) 8 12394809 At_Far-red-induction 20001450Organism A. thaliana 12394809 At_Far-red-induction 20001450 Plant LineColumbia 12394809 At_Far-red-induction 20001450 Light Far-red vs. White12394809 At_Far-red-induction 20001450 Tissue Whole Plant 12394809At_Far-red-induction 20001451 Age (day) 8 12394809 At_Far-red-induction20001451 Timepoint (hr) 24 12394809 At_Far-red-induction 20001451Organism A. thaliana 12394809 At_Far-red-induction 20001451 Plant LineColumbia 12394809 At_Far-red-induction 20001451 Light Far-red vs. White12394809 At_Far-red-induction 20001451 Tissue Whole Plant 12394809At_Drought_Soil_Dry 20001554 Timepoint (day) 7 12394809At_Drought_Soil_Dry 20001554 Age (day) 21 12394809 At_Drought_Soil_Dry20001554 Organism A. thaliana 12394809 At_Drought_Soil_Dry 20001554Treatment Drought vs. No Drought 12394809 At_Drought_Soil_Dry 20001554Post Timepoint (hr) None 12394809 At_Drought_Soil_Dry 20001554Post-Treatment None 12394809 At_Drought_Soil_Dry 20001554 Plant Line WS12394809 At_Drought_Soil_Dry 20001555 Timepoint (day) 10 12394809At_Drought_Soil_Dry 20001555 Age (day) 24 12394809 At_Drought_Soil_Dry20001555 Organism A. thaliana 12394809 At_Drought_Soil_Dry 20001555Treatment Drought vs. No Drought 12394809 At_Drought_Soil_Dry 20001555Post Timepoint (hr) None 12394809 At_Drought_Soil_Dry 20001555Post-Treatment None 12394809 At_Drought_Soil_Dry 20001555 Plant Line WS12394809 At_Drought_Soil_Dry 20001556 Timepoint (day) 12 12394809At_Drought_Soil_Dry 20001556 Age (day) 26 12394809 At_Drought_Soil_Dry20001556 Organism A. thaliana 12394809 At_Drought_Soil_Dry 20001556Treatment Drought vs. No Drought 12394809 At_Drought_Soil_Dry 20001556Post Timepoint (hr) None 12394809 At_Drought_Soil_Dry 20001556Post-Treatment None 12394809 At_Drought_Soil_Dry 20001556 Plant Line WS12394809 At_Drought_Soil_Dry 20001559 Timepoint (day) 14 12394809At_Drought_Soil_Dry 20001559 Age (day) 28 12394809 At_Drought_Soil_Dry20001559 Post Timepoint (hr) 29 12394809 At_Drought_Soil_Dry 20001559Organism A. thaliana 12394809 At_Drought_Soil_Dry 20001559 TreatmentDrought vs. No Drought 12394809 At_Drought_Soil_Dry 20001559Post-Treatment Re-Water vs. No Drought 12394809 At_Drought_Soil_Dry20001559 Plant Line WS 12394809 At_Interploidy_Crosses 20001853 Age(day) 5 12394809 At_Interploidy_Crosses 20001853 Organism A. thaliana12394809 At_Interploidy_Crosses 20001853 Plant Line Columbia 12394809At_Interploidy_Crosses 20001853 Cross Fis1 vs. 2X × 2X 12394809At_Interploidy_Crosses 20001853 Tissue Siliques 12394809At_Drought_Reproduction 20001904 Timepoint (day) 7 12394809At_Drought_Reproduction 20001904 Age (day) 37 12394809At_Drought_Reproduction 20001904 Organism A. thaliana 12394809At_Drought_Reproduction 20001904 Treatment Drought vs. No Drought12394809 At_Drought_Reproduction 20001904 Tissue Rosettes 12394809At_Drought_Reproduction 20001904 Plant Line WS 12394809At_Drought_Reproduction 20001911 Timepoint (day) 10 12394809At_Drought_Reproduction 20001911 Age (day) 40 12394809At_Drought_Reproduction 20001911 Organism A. thaliana 12394809At_Drought_Reproduction 20001911 Treatment Drought vs. No Drought12394809 At_Drought_Reproduction 20001911 Tissue Flowers 12394809At_Drought_Reproduction 20001911 Plant Line WS 12394809 At_8deg_Cold20002107 Age (day) 11 12394809 At_8deg_Cold 20002107 Timepoint (hr) 9612394809 At_8deg_Cold 20002107 Temperature (deg C.) 8 vs. 22 12394809At_8deg_Cold 20002107 Organism A. thaliana 12394809 At_8deg_Cold20002107 Tissue Whole Plant 12394809 At_8deg_Cold 20002107 Plant Line WSPromoter YP0337 Modulates the gene: Unknown protein. The GenBankdescription of the gene: NM_101546 Arabidopsis thaliana expressedprotein (At1g16850) mRNA, complete cdsgi|18394408|ref|NM_101546.1|[18394408] The promoter sequence:5′acttattagtttaggtttccatcacctatttaattcgtaattcttatacatgcatataatagagatacatatatacaaatttatgatcatttttgcacaacatgtgatctcattcattagtatgcattatgcgaaaacctcgacgcgcaaaagacacgtaatagctaataatgttactcatttataatgattgaagcaagacgaaaacaacaacatatatatcaaattgtaaactagatatttcttaaaagtgaaaaaaaacaaagaaatataaaggacaattttgagtcagtctcttaatattaaaacatatatacataaataagcacaaacgtggttacctgtcttcatgcaatgtggactttagtttatctaatcaaaatcaaaataaaaggtgtaatagttctcgtcatttttcaaattttaaaaatcagaaccaagtgatttttgtttgagtattgatccattgtttaaacaatttaacacagtatatacgtctcttgagatgttgacatgatgataaaatacgagatcgtctcttggttttcgaattttgaactttaatagtttttttttttagggaaactttaatagttgtttatcataagattagtcacctaatggttacgttgcagtaccgaaccaattttttacccttttttctaaatgtggtcgtggcataatttccaaaagagatccaaaacccggtttgctcaactgataagccggtcggttctggtttgaaaaacaagaaataatctgaaagtgtgaaacagcaacgtgtctcggtgtttcatgagccacctgccacctcattcacgtcggtcattttgtcgtttcacggttcacgctctagacacgtgctctgtccccaccatgactttcgctgccgactcgcttcgctttgcaaactcaaacatgtgtgTATAtgtaagtttcatcctaataag 3′-caaagaaaacatcaaaATG The promoter wascloned from the organism: Arabidopsis thaliana, WS ecotype Alternativenucleotides: Predicted (Columbia) Experimental (Wassilewskija) Sequence(bp) Mismatch Columbia/Wassilewskija 597 SNP t/c 996 SNP t/a Thepromoter was cloned in the vector: pNewbin4-HAP1-GFP When cloned intothe vector the promoter was operably linked to a marker, which was thetype: GFP-ER Promoter-marker vector was tested in: Arabidopsis thaliana,WS ecotype Generation screened: XT1 Mature XT2 Seedling T2 Mature T3Seedling The spatial expression of the promoter-marker vector was foundobserved in and would be useful in expression in any or all of thefollowing: Primary Root    L epidermis L trichoblast L atrichoblast Lroot hair Observed expression pattern of the promoter-marker vector wasin: T1 mature: No expression. T2 seedling: Low expression in rootepidermal cells at transition zone decreasing to expression in singlecells at mid root Misc. promoter information: Bidirectionality:Pass Exons: Pass   Repeats: No The Ceres cDNA ID of the endogenouscoding sequence to the promoter: 12326510 cDNA nucleotide sequence:ACCACATTAATTTAAAACAAAGAAAACATCAAAATGGCTGAAAAAGTAAAGTCTGGTCAAGTTTTTAACCTATTATGCATATTCTCGATCTTTTTCTTCCTCTTTGTGTTATCAGTGAATGTTTCGGCTGATGTCGATTCTGAGAGAGCGGTGCCATCTGAAGATAAAACGACGACTGTTTGGCTAACTAAAATCAAACGGTCCGGTAAAAATTATTGGGCTAAAGTTAGAGAGACTTTGGATCGTGGACAGTCCCACTTCTTTCCTCCGAACACATATTTTACCGGAAAGAATGATGCGCCGATGGGAGCCGGTGAAAATATGAAAGAGGCGGCGACGAGGAGCTTTGAGCATAGCAAAGCGACGGTGGAGGAAGCTGCTAGATCAGCGGCAGAAGTGGTGAGTGATACGGCGGAAGCTGTGAAAGAAAAGGTGAAGAGGAGCGTTTCCGGTGGAGTGACGCAGCCGTCGGAGGGATCTGAGGAGCTATAAATACGCAGTTGTTCTAAGCTTATGGGTTTTAATTATTTAAATAATTAGTGTGTGTTTGAGATCAAAATGACACAGTTTTGGGGGAGTATATCTCCACATCATATGTTGTTTGCATCACATGGTTTCTCTGTATACAACGACCAGATCCACATCACTCATTCTCGTCCTTCTTTTTGTCATGAATACAGAATAATATTTTAGATT CTACCoding sequence:MAEKVKSGQVFNLLCIFSIFFFLFVLSVNVSADVDSERAVPSEDKTTTVWLTKIKRSGKNYWAKVRETLDRGQSHFFPPNTYFTGKNDAPMGAGENMKEAATRSFEHSKATVEEAARSAAEVVSDTAEAVKEKVKRSVSGGVTQPSEGSEEL* Microarray data shows that the coding sequencewas expressed in the following experiments, which shows that thepromoter would be useful to modulate expression in situations similar tothe following: CDNA_ID SHORT_NAME EXPT_REP_ID IS_UP 12326510At_Germinating_Seeds 108461 − 12326510 At_Germinating_Seeds 108462 −12326510 At_Germinating_Seeds 108464 − 12326510 At_Drought_Flowers108473 + 12326510 At_ap2_floral_buds 108501 − 12326510 At_100 uM_ABA108560 + 12326510 At_100 uM_ABA 108561 + 12326510 At_Drought 108572 +12326510 At_Drought 108573 + 12326510 At_Wounding 108574 + 12326510At_4deg_Cold 108579 + 12326510 At_15 mM_NH4NO3_L-to-H 108588 − 12326510At_15 mM_NH4NO3_L-to-H 108589 − 12326510 At_15 mM_NH4NO3_L-to-H 108590 −12326510 At_15 mM_NH4NO3_L-to-H 108591 − 12326510 At_Ler-rhl_Root108594 + 12326510 At_Ler-pi_Ovule 108595 + 12326510 At_100 uM_ABA108605 + 12326510 At_100 uM_ABA 108606 + 12326510 At_100 uM_ABA 108607 +12326510 At_100 uM_ABA 108608 + 12326510 At_100 uM_ABA 108609 + 12326510At_100 uM_ABA_Mutants 108624 − 12326510 At_100 uM_ABA_Mutants 20000069 +12326510 At_100 uM_ABA_Mutants 20000070 + 12326510 At_100 uM_ABA_Mutants20000071 + 12326510 At_100 uM_ABA_Mutants 20000072 + 12326510 At_100uM_ABA_Mutants 20000086 + 12326510 At_100 uM_ABA_Mutants 20000087 +12326510 At_100 uM_ABA_Mutants 20000088 + 12326510 At_2mM_SA_CS3726-Columbia 20000089 + 12326510 At_2 mM_SA_CS3726-Columbia20000090 + 12326510 At_100 uM_ABA_Mutants 20000117 + 12326510 At_100uM_ABA 20000166 + 12326510 At_100 uM_ABA 20000169 + 12326510At_Germinating_Seeds 20000179 − 12326510 At_Germinating_Seeds 20000180 −12326510 At_Shoots 20000184 − 12326510 At_Root-Tips-vs-Tops 20000227 +12326510 At_Drought 20000267 + 12326510 At_100 mM_NaCl 20000268 +12326510 At_100 mM_NaCl 20000308 + 12326510 At_Drought 20000436 +12326510 At_Drought 20000437 + 12326510 At_1 uM_BR-BRZ 20000441 −12326510 At_1 uM_BR-BRZ 20000443 − 12326510 At_100 uM_ABA 20000453 +12326510 At_Guard_Cells 20000495 − 12326510 At_100 uM_ABA_Mutants20000573 − 12326510 At_100 uM_ABA_Mutants 20000574 − 12326510 At_100uM_ABA_Mutants 20000575 + 12326510 At_100 uM_ABA_Mutants 20000576 +12326510 At_15 mM_NH4NO3_L-to-H 20000709 − 12326510 At_Far-red-induction20001248 + 12326510 At_Line_Comparisons 20001309 − 12326510At_Line_Comparisons 20001310 − 12326510 At_Far-red-induction 20001450 +12326510 At_Far-red-induction 20001451 + 12326510 At_Drought_Soil_Dry20001553 + 12326510 At_Drought_Soil_Dry 20001554 + 12326510At_Drought_Soil_Dry 20001555 + 12326510 At_Drought_Soil_Dry 20001556 +12326510 At_Drought_Soil_Dry 20001557 + 12326510 At_Drought_Soil_Dry20001559 + 12326510 At_Far-red-enriched-adult 20001770 + 12326510At_Interploidy_Crosses 20001853 + 12326510 At_Drought_Reproduction20001904 + 12326510 At_Drought_Reproduction 20001905 + 12326510At_Drought_Reproduction 20001906 + 12326510 At_Drought_Reproduction20001907 + 12326510 At_Drought_Reproduction 20001908 + 12326510At_Drought_Reproduction 20001911 + 12326510 At_Line_Comparisons20002009 + 12326510 At_8deg_Cold 20002105 + 12326510 At_8deg_Cold20002107 + 12326510 At_8deg_Cold 20002108 + 12326510 At_8deg_Cold20002109 + The parameters for the microarray experiments listed above byExpt_Rep_ID and Short_Name are as follow below: CDNA_ID SHORT_NAMEEXPT_REP_ID PARAM_NAME VALUE 12326510 At_Germinating_Seeds 108461 Age(day) 1 vs. 0 12326510 At_Germinating_Seeds 108461 Tissue GerminatingSeeds 12326510 At_Germinating_Seeds 108462 Age (day) 2 vs. 0 12326510At_Germinating_Seeds 108462 Tissue Germinating Seeds 12326510At_Germinating_Seeds 108464 Age (day) 4 vs. 0 12326510At_Germinating_Seeds 108464 Tissue Germinating Seeds 12326510At_Drought_Flowers 108473 Timepoint (hr) 7 d 12326510 At_Drought_Flowers108473 Treatment Drought vs. No Drought 12326510 At_Drought_Flowers108473 Tissue Flower 12326510 At_ap2_floral_buds 108501 Plant Line ap2(Ler.) 12326510 At_ap2_floral_buds 108501 Tissue Closed Flower 12326510At_100 uM_ABA 108560 Timepoint (hr) 1 12326510 At_100 uM_ABA 108560Treatment 100 uM ABA vs. No Treatment 12326510 At_100 uM_ABA 108560Tissue Aerial 12326510 At_100 uM_ABA 108561 Timepoint (hr) 6 12326510At_100 uM_ABA 108561 Treatment 100 uM ABA vs. No Treatment 12326510At_100 uM_ABA 108561 Tissue Aerial 12326510 At_Drought 108572 Timepoint(hr) 1 12326510 At_Drought 108572 Tissue Aerial 12326510 At_Drought108572 Treatment Drought vs. No Drought 12326510 At_Drought 108573Timepoint (hr) 6 12326510 At_Drought 108573 Tissue Aerial 12326510At_Drought 108573 Treatment Drought vs. No Drought 12326510 At_Wounding108574 Timepoint (hr) 1 12326510 At_Wounding 108574 Tissue Aerial12326510 At_Wounding 108574 Treatment Wounding vs. No Wounding 12326510At_4deg_Cold 108579 Timepoint (hr) 6 12326510 At_4deg_Cold 108579Temperature 4 vs. 22 (deg C.) 12326510 At_4deg_Cold 108579 Tissue Aerial12326510 At_15mM_NH4NO3_L-to-H 108588 Timepoint (hr) 2 12326510At_15mM_NH4NO3_L-to-H 108588 Treatment 15 mM NH4NO3 vs. 30 mM Mannitol12326510 At_15mM_NH4NO3_L-to-H 108588 Tissue Aerial 12326510At_15mM_NH4NO3_L-to-H 108589 Timepoint (hr) 6 12326510At_15mM_NH4NO3_L-to-H 108589 Treatment 15 mM NH4NO3 vs. 30 mM Mannitol12326510 At_15mM_NH4NO3_L-to-H 108589 Tissue Aerial 12326510At_15mM_NH4NO3_L-to-H 108590 Timepoint (hr) 9 12326510At_15mM_NH4NO3_L-to-H 108590 Treatment 15 mM NH4NO3 vs. 30 mM Mannitol12326510 At_15mM_NH4NO3_L-to-H 108590 Tissue Aerial 12326510At_15mM_NH4NO3_L-to-H 108591 Timepoint (hr) 12 12326510At_15mM_NH4NO3_L-to-H 108591 Treatment 15 mM NH4NO3 vs. 30 mM Mannitol12326510 At_15mM_NH4NO3_L-to-H 108591 Tissue Aerial 12326510At_Ler-rhl_Root 108594 Plant Line Ler_rhl 12326510 At_Ler-rhl_Root108594 Tissue Roots 12326510 At_Ler-pi_Ovule 108595 Plant Line Ler_pi12326510 At_Ler-pi_Ovule 108595 Tissue Ovules 12326510 At_100 uM_ABA108605 Timepoint (hr) 6 12326510 At_100 uM_ABA 108605 Treatment 100 uMABA vs. No Treatment 12326510 At_100 uM_ABA 108605 Tissue Aerial12326510 At_100 uM_ABA 108606 Timepoint (hr) 2 12326510 At_100 uM_ABA108606 Treatment 100 uM ABA vs. No Treatment 12326510 At_100 uM_ABA108606 Tissue Aerial 12326510 At_100 uM_ABA 108607 Timepoint (hr) 412326510 At_100 uM_ABA 108607 Treatment 100 uM ABA vs. No Treatment12326510 At_100 uM_ABA 108607 Tissue Aerial 12326510 At_100 uM_ABA108608 Timepoint (hr) 1 12326510 At_100 uM_ABA 108608 Treatment 100 uMABA vs. No Treatment 12326510 At_100 uM_ABA 108608 Tissue Aerial12326510 At_100 uM_ABA 108609 Timepoint (hr) 24 12326510 At_100 uM_ABA108609 Treatment 100 uM ABA vs. No Treatment 12326510 At_100 uM_ABA108609 Tissue Aerial 12326510 At_100 uM_ABA_Mutants 108624 Timepoint(hr) 6 12326510 At_100 uM_ABA_Mutants 108624 Treatment 100 uM ABA vs. NoTreatment 12326510 At_100 uM_ABA_Mutants 108624 Tissue Aerial 12326510At_100 uM_ABA_Mutants 108624 Plant Line CS8105 12326510 At_100uM_ABA_Mutants 20000069 Timepoint (hr) 6 12326510 At_100 uM_ABA_Mutants20000069 Treatment 100 uM ABA vs. No Treatment 12326510 At_100uM_ABA_Mutants 20000069 Tissue Aerial 12326510 At_100 uM_ABA_Mutants20000069 Plant Line CS23 12326510 At_100 uM_ABA_Mutants 20000070Timepoint (hr) 6 12326510 At_100 uM_ABA_Mutants 20000070 Treatment 100uM ABA vs. No Treatment 12326510 At_100 uM_ABA_Mutants 20000070 TissueAerial 12326510 At_100 uM_ABA_Mutants 20000070 Plant Line CS24 12326510At_100 uM_ABA_Mutants 20000071 Timepoint (hr) 6 12326510 At_100uM_ABA_Mutants 20000071 Treatment 100 uM ABA vs. No Treatment 12326510At_100 uM_ABA_Mutants 20000071 Tissue Aerial 12326510 At_100uM_ABA_Mutants 20000071 Plant Line CS8104 12326510 At_100 uM_ABA_Mutants20000072 Timepoint (hr) 6 12326510 At_100 uM_ABA_Mutants 20000072Treatment 100 uM ABA vs. No Treatment 12326510 At_100 uM_ABA_Mutants20000072 Tissue Aerial 12326510 At_100 uM_ABA_Mutants 20000072 PlantLine CS8105 12326510 At_100 uM_ABA_Mutants 20000086 Timepoint (hr) 612326510 At_100 uM_ABA_Mutants 20000086 Treatment 100 uM ABA vs. NoTreatment 12326510 At_100 uM_ABA_Mutants 20000086 Tissue Aerial 12326510At_100 uM_ABA_Mutants 20000086 Plant Line CS22 12326510 At_100uM_ABA_Mutants 20000087 Timepoint (hr) 6 12326510 At_100 uM_ABA_Mutants20000087 Treatment 100 uM ABA vs. No Treatment 12326510 At_100uM_ABA_Mutants 20000087 Tissue Aerial 12326510 At_100 uM_ABA_Mutants20000087 Plant Line WS 12326510 At_100 uM_ABA_Mutants 20000088 Timepoint(hr) 6 12326510 At_100 uM_ABA_Mutants 20000088 Treatment 100 uM ABA vs.No Treatment 12326510 At_100 uM_ABA_Mutants 20000088 Tissue Aerial12326510 At_100 uM_ABA_Mutants 20000088 Plant Line Landsberg 12326510At_2mM_SA_CS3726- 20000089 Timepoint (hr) 6 Columbia 12326510At_2mM_SA_CS3726- 20000089 Treatment 2 mM SA vs. Columbia No Treatment12326510 At_2mM_SA_CS3726- 20000089 Tissue Aerial Columbia 12326510At_2mM_SA_CS3726- 20000089 Plant Line CS3726 Columbia 12326510At_2mM_SA_CS3726- 20000090 Timepoint (hr) 6 Columbia 12326510At_2mM_SA_CS3726- 20000090 Treatment 2 mM SA vs. Columbia No Treatment12326510 At_2mM_SA_CS3726- 20000090 Tissue Aerial Columbia 12326510At_2mM_SA_CS3726- 20000090 Plant Line Columbia Columbia 12326510 At_100uM_ABA_Mutants 20000117 Timepoint (hr) 6 12326510 At_100 uM_ABA_Mutants20000117 Treatment 100 uM ABA vs. No Treatment 12326510 At_100uM_ABA_Mutants 20000117 Tissue Aerial 12326510 At_100 uM_ABA_Mutants20000117 Plant Line Columbia 12326510 At_100 uM_ABA 20000166 Timepoint(hr) 1 12326510 At_100 uM_ABA 20000166 Age (day) 14 12326510 At_100uM_ABA 20000166 Treatment 100 uM ABA vs. No Treatment 12326510 At_100uM_ABA 20000166 Organism A. thaliana 12326510 At_100 uM_ABA 20000166Tissue Aerial 12326510 At_100 uM_ABA 20000166 Plant Line WS 12326510At_100 uM_ABA 20000169 Timepoint (hr) 6 12326510 At_100 uM_ABA 20000169Age (day) 14 12326510 At_100 uM_ABA 20000169 Treatment 100 uM ABA vs. NoTreatment 12326510 At_100 uM_ABA 20000169 Organism A. thaliana 12326510At_100 uM_ABA 20000169 Tissue Aerial 12326510 At_100 uM_ABA 20000169Plant Line WS 12326510 At_Germinating_Seeds 20000179 Age (hr) 6 vs. 012326510 At_Germinating_Seeds 20000179 Organism A. thaliana 12326510At_Germinating_Seeds 20000179 Tissue Germinating Seeds 12326510At_Germinating_Seeds 20000179 Plant Line WS 12326510At_Germinating_Seeds 20000180 Age (hr) 24 vs. 0 12326510At_Germinating_Seeds 20000180 Organism A. thaliana 12326510At_Germinating_Seeds 20000180 Tissue Germinating Seeds 12326510At_Germinating_Seeds 20000180 Plant Line WS 12326510 At_Shoots 20000184Age (day) 7 vs. 21 12326510 At_Shoots 20000184 Organism A. thaliana12326510 At_Shoots 20000184 Tissue Shoots vs. Whole Plant 12326510At_Shoots 20000184 Plant Line WS 12326510 At_Root-Tips-vs-Tops 20000227Age (day) 7, 10, 14 12326510 At_Root-Tips-vs-Tops 20000227 Organism A.thaliana 12326510 At_Root-Tips-vs-Tops 20000227 Tissue Root Tips vs.Root Tops 12326510 At_Root-Tips-vs-Tops 20000227 Plant Line WS 12326510At_Drought 20000267 Timepoint (hr) 6 12326510 At_Drought 20000267 Age(day) 7 12326510 At_Drought 20000267 Organism A. thaliana 12326510At_Drought 20000267 Treatment Drought vs. No Drought 12326510 At_Drought20000267 Tissue Whole Plant 12326510 At_Drought 20000267 Plant Line WS12326510 At_100mM_NaCl 20000268 Timepoint (hr) 6 12326510 At_100mM_NaCl20000268 Age (day) 14 12326510 At_100mM_NaCl 20000268 Treatment 100 mMNaCl vs. No Treatment 12326510 At_100mM_NaCl 20000268 Organism A.thaliana 12326510 At_100mM_NaCl 20000268 Tissue Whole Plant 12326510At_100mM_NaCl 20000268 Plant Line WS 12326510 At_100mM_NaCl 20000308 Age(day) 17 12326510 At_100mM_NaCl 20000308 Timepoint (hr) 72 12326510At_100mM_NaCl 20000308 Treatment 100 mM NaCl vs. No Treatment 12326510At_100mM_NaCl 20000308 Organism A. thaliana 12326510 At_100mM_NaCl20000308 Tissue Whole Plant 12326510 At_100mM_NaCl 20000308 Plant LineWS 12326510 At_Drought 20000436 Age (day) 7 12326510 At_Drought 20000436Timepoint (hr) 12 12326510 At_Drought 20000436 Organism A. thaliana12326510 At_Drought 20000436 Treatment Drought vs. No Drought 12326510At_Drought 20000436 Tissue Whole Plant 12326510 At_Drought 20000436Plant Line WS 12326510 At_Drought 20000437 Age (day) 8 12326510At_Drought 20000437 Timepoint (hr) 24 12326510 At_Drought 20000437Organism A. thaliana 12326510 At_Drought 20000437 Treatment Drought vs.No Drought 12326510 At_Drought 20000437 Tissue Whole Plant 12326510At_Drought 20000437 Plant Line WS 12326510 At_1 uM_BR-BRZ 20000441Treatment 1 uM BR vs. No Treatment 12326510 At_1 uM_BR-BRZ 20000441Tissue Shoot Apices 12326510 At_1 uM_BR-BRZ 20000443 Treatment 1 uM BRZvs. No Treatment 12326510 At_1 uM_BR-BRZ 20000443 Tissue Shoot Apices12326510 At_100 uM_ABA 20000453 Age (day) 15 12326510 At_100 uM_ABA20000453 Timepoint (hr) 24 12326510 At_100 uM_ABA 20000453 Treatment 100uM ABA vs. No Treatment 12326510 At_100 uM_ABA 20000453 Organism A.thaliana 12326510 At_100 uM_ABA 20000453 Tissue Aerial 12326510 At_100uM_ABA 20000453 Plant Line WS 12326510 At_Guard_Cells 20000495 HarvestDate Aug. 2, 2002 12326510 At_Guard_Cells 20000495 Organism A. thaliana12326510 At_Guard_Cells 20000495 Tissue Guard Cells vs. Leaves 12326510At_100 uM_ABA_Mutants 20000573 Organism A. thaliana 12326510 At_100uM_ABA_Mutants 20000573 Plant Line CS22 vs. Ler wt 12326510 At_100uM_ABA_Mutants 20000573 Timepoint (hr) N/A 12326510 At_100uM_ABA_Mutants 20000573 Treatment None 12326510 At_100 uM_ABA_Mutants20000573 Tissue Whole Plant 12326510 At_100 uM_ABA_Mutants 20000574Organism A. thaliana 12326510 At_100 uM_ABA_Mutants 20000574 Plant LineCS23 vs. Ler wt 12326510 At_100 uM_ABA_Mutants 20000574 Timepoint (hr)N/A 12326510 At_100 uM_ABA_Mutants 20000574 Treatment None 12326510At_100 uM_ABA_Mutants 20000574 Tissue Whole Plant 12326510 At_100uM_ABA_Mutants 20000575 Timepoint (hr) 6 12326510 At_100 uM_ABA_Mutants20000575 Treatment 1 uM ABA vs. No Treatment 12326510 At_100uM_ABA_Mutants 20000575 Organism A. thaliana 12326510 At_100uM_ABA_Mutants 20000575 Plant Line CS22 12326510 At_100 uM_ABA_Mutants20000575 Tissue Whole Plant 12326510 At_100 uM_ABA_Mutants 20000576Timepoint (hr) 6 12326510 At_100 uM_ABA_Mutants 20000576 Treatment 1 uMABA vs. No Treatment 12326510 At_100 uM_ABA_Mutants 20000576 Organism A.thaliana 12326510 At_100 uM_ABA_Mutants 20000576 Plant Line CS2312326510 At_100 uM_ABA_Mutants 20000576 Tissue Whole Plant 12326510At_15mM_NH4NO3_L-to-H 20000709 Timepoint (hr) 4 12326510At_15mM_NH4NO3_L-to-H 20000709 Age (hr) 14 12326510At_15mM_NH4NO3_L-to-H 20000709 Treatment 15 mM NH4NO3 vs. 30 mM Mannitol12326510 At_15mM_NH4NO3_L-to-H 20000709 Organism A. thaliana 12326510At_15mM_NH4NO3_L-to-H 20000709 Tissue Aerial 12326510At_15mM_NH4NO3_L-to-H 20000709 Plant Line WS 12326510At_Far-red-induction 20001248 Timepoint (hr) 4 12326510At_Far-red-induction 20001248 Age (day) 7 12326510 At_Far-red-induction20001248 Organism A. thaliana 12326510 At_Far-red-induction 20001248Plant Line Columbia 12326510 At_Far-red-induction 20001248 Light Far-redvs. White 12326510 At_Far-red-induction 20001248 Tissue Whole Plant12326510 At_Line_Comparisons 20001309 Plant Line WBin4- WX49R-A vs. WS12326510 At_Line_Comparisons 20001310 Plant Line WBin4-WX17- A vs. WS12326510 At_Far-red-induction 20001450 Age (day) 7 12326510At_Far-red-induction 20001450 Timepoint (hr) 8 12326510At_Far-red-induction 20001450 Organism A. thaliana 12326510At_Far-red-induction 20001450 Plant Line Columbia 12326510At_Far-red-induction 20001450 Light Far-red vs. White 12326510At_Far-red-induction 20001450 Tissue Whole Plant 12326510At_Far-red-induction 20001451 Age (day) 8 12326510 At_Far-red-induction20001451 Timepoint (hr) 24 12326510 At_Far-red-induction 20001451Organism A. thaliana 12326510 At_Far-red-induction 20001451 Plant LineColumbia 12326510 At_Far-red-induction 20001451 Light Far-red vs. White12326510 At_Far-red-induction 20001451 Tissue Whole Plant 12326510At_Drought_Soil_Dry 20001553 Timepoint (day) 5 12326510At_Drought_Soil_Dry 20001553 Age (day) 19 12326510 At_Drought_Soil_Dry20001553 Organism A. thaliana 12326510 At_Drought_Soil_Dry 20001553Treatment Drought vs. No Drought 12326510 At_Drought_Soil_Dry 20001553Post Timepoint None (hr) 12326510 At_Drought_Soil_Dry 20001553Post-Treatment None 12326510 At_Drought_Soil_Dry 20001553 Plant Line WS12326510 At_Drought_Soil_Dry 20001554 Timepoint (day) 7 12326510At_Drought_Soil_Dry 20001554 Age (day) 21 12326510 At_Drought_Soil_Dry20001554 Organism A. thaliana 12326510 At_Drought_Soil_Dry 20001554Treatment Drought vs. No Drought 12326510 At_Drought_Soil_Dry 20001554Post Timepoint None (hr) 12326510 At_Drought_Soil_Dry 20001554Post-Treatment None 12326510 At_Drought_Soil_Dry 20001554 Plant Line WS12326510 At_Drought_Soil_Dry 20001555 Timepoint (day) 10 12326510At_Drought_Soil_Dry 20001555 Age (day) 24 12326510 At_Drought_Soil_Dry20001555 Organism A. thaliana 12326510 At_Drought_Soil_Dry 20001555Treatment Drought vs. No Drought 12326510 At_Drought_Soil_Dry 20001555Post Timepoint None (hr) 12326510 At_Drought_Soil_Dry 20001555Post-Treatment None 12326510 At_Drought_Soil_Dry 20001555 Plant Line WS12326510 At_Drought_Soil_Dry 20001556 Timepoint (day) 12 12326510At_Drought_Soil_Dry 20001556 Age (day) 26 12326510 At_Drought_Soil_Dry20001556 Organism A. thaliana 12326510 At_Drought_Soil_Dry 20001556Treatment Drought vs. No Drought 12326510 At_Drought_Soil_Dry 20001556Post Timepoint None (hr) 12326510 At_Drought_Soil_Dry 20001556Post-Treatment None 12326510 At_Drought_Soil_Dry 20001556 Plant Line WS12326510 At_Drought_Soil_Dry 20001557 Post Timepoint 3 (hr) 12326510At_Drought_Soil_Dry 20001557 Timepoint (day) 13 12326510At_Drought_Soil_Dry 20001557 Age (day) 27 12326510 At_Drought_Soil_Dry20001557 Organism A. thaliana 12326510 At_Drought_Soil_Dry 20001557Treatment Drought vs. No Drought 12326510 At_Drought_Soil_Dry 20001557Post-Treatment Re-Water vs. No Drought 12326510 At_Drought_Soil_Dry20001557 Plant Line WS 12326510 At_Drought_Soil_Dry 20001559 Timepoint(day) 14 12326510 At_Drought_Soil_Dry 20001559 Age (day) 28 12326510At_Drought_Soil_Dry 20001559 Post Timepoint 29 (hr) 12326510At_Drought_Soil_Dry 20001559 Organism A. thaliana 12326510At_Drought_Soil_Dry 20001559 Treatment Drought vs. No Drought 12326510At_Drought_Soil_Dry 20001559 Post-Treatment Re-Water vs. No Drought12326510 At_Drought_Soil_Dry 20001559 Plant Line WS 12326510At_Far-red-enriched-adult 20001770 Timepoint (hr) 8 12326510At_Far-red-enriched-adult 20001770 Age (day) 28 12326510At_Far-red-enriched-adult 20001770 Organism A. thaliana 12326510At_Far-red-enriched-adult 20001770 Tissue Aerial 12326510At_Far-red-enriched-adult 20001770 Plant Line Columbia 12326510At_Far-red-enriched-adult 20001770 Light Far-red enriched vs. White12326510 At_Interploidy_Crosses 20001853 Age (day) 5 12326510At_Interploidy_Crosses 20001853 Organism A. thaliana 12326510At_Interploidy_Crosses 20001853 Plant Line Columbia 12326510At_Interploidy_Crosses 20001853 Cross Fis1 vs. 2X × 2X 12326510At_Interploidy_Crosses 20001853 Tissue Siliques 12326510At_Drought_Reproduction 20001904 Timepoint (day) 7 12326510At_Drought_Reproduction 20001904 Age (day) 37 12326510At_Drought_Reproduction 20001904 Organism A. thaliana 12326510At_Drought_Reproduction 20001904 Treatment Drought vs. No Drought12326510 At_Drought_Reproduction 20001904 Tissue Rosettes 12326510At_Drought_Reproduction 20001904 Plant Line WS 12326510At_Drought_Reproduction 20001905 Timepoint (day) 10 12326510At_Drought_Reproduction 20001905 Age (day) 40 12326510At_Drought_Reproduction 20001905 Organism A. thaliana 12326510At_Drought_Reproduction 20001905 Treatment Drought vs. No Drought12326510 At_Drought_Reproduction 20001905 Tissue Rosettes 12326510At_Drought_Reproduction 20001905 Plant Line WS 12326510At_Drought_Reproduction 20001906 Timepoint (day) 5 12326510At_Drought_Reproduction 20001906 Age (day) 35 12326510At_Drought_Reproduction 20001906 Organism A. thaliana 12326510At_Drought_Reproduction 20001906 Treatment Drought vs. No Drought12326510 At_Drought_Reproduction 20001906 Tissue Siliques 12326510At_Drought_Reproduction 20001906 Plant Line WS 12326510At_Drought_Reproduction 20001907 Timepoint (day) 7 12326510At_Drought_Reproduction 20001907 Age (day) 37 12326510At_Drought_Reproduction 20001907 Organism A. thaliana 12326510At_Drought_Reproduction 20001907 Treatment Drought vs. No Drought12326510 At_Drought_Reproduction 20001907 Plant Line WS 12326510At_Drought_Reproduction 20001908 Timepoint (day) 10 12326510At_Drought_Reproduction 20001908 Age (day) 40 12326510At_Drought_Reproduction 20001908 Organism A. thaliana 12326510At_Drought_Reproduction 20001908 Treatment Drought vs. No Drought12326510 At_Drought_Reproduction 20001908 Tissue Siliques 12326510At_Drought_Reproduction 20001908 Plant Line WS 12326510At_Drought_Reproduction 20001911 Timepoint (day) 10 12326510At_Drought_Reproduction 20001911 Age (day) 40 12326510At_Drought_Reproduction 20001911 Organism A. thaliana 12326510At_Drought_Reproduction 20001911 Treatment Drought vs. No Drought12326510 At_Drought_Reproduction 20001911 Tissue Flowers 12326510At_Drought_Reproduction 20001911 Plant Line WS 12326510At_Line_Comparisons 20002009 Plant Line ME01642 vs. WS 12326510At_8deg_Cold 20002105 Age (day) 7 12326510 At_8deg_Cold 20002105Timepoint (hr) 8 12326510 At_8deg_Cold 20002105 Temperature 8 vs. 22(deg C.) 12326510 At_8deg_Cold 20002105 Organism A. thaliana 12326510At_8deg_Cold 20002105 Tissue Whole Plant 12326510 At_8deg_Cold 20002105Plant Line WS 12326510 At_8deg_Cold 20002107 Age (day) 11 12326510At_8deg_Cold 20002107 Timepoint (hr) 96 12326510 At_8deg_Cold 20002107Temperature 8 vs. 22 (deg C.) 12326510 At_8deg_Cold 20002107 Organism A.thaliana 12326510 At_8deg_Cold 20002107 Tissue Whole Plant 12326510At_8deg_Cold 20002107 Plant Line WS 12326510 At_8deg_Cold 20002108 Age(day) 14 12326510 At_8deg_Cold 20002108 Timepoint (hr) 168 12326510At_8deg_Cold 20002108 Temperature 8 vs. 22 (deg C.) 12326510At_8deg_Cold 20002108 Organism A. thaliana 12326510 At_8deg_Cold20002108 Tissue Whole Plant 12326510 At_8deg_Cold 20002108 Plant Line WS12326510 At_8deg_Cold 20002109 Age (day) 16 12326510 At_8deg_Cold20002109 Timepoint (hr) 216 12326510 At_8deg_Cold 20002109 Temperature 8vs. 22 (deg C.) 12326510 At_8deg_Cold 20002109 Organism A. thaliana12326510 At_8deg_Cold 20002109 Tissue Whole Plant 12326510 At_8deg_Cold20002109 Plant Line WS Promoter YP0289 Modulates the gene: phi-1-relatedprotein The GenBank description of the gene: NM_125822 Arabidopsisthaliana phi-1-related protein (At5g64260) mRNA, complete cdsgi|30697983|ref|NM_125822.2|[30697983] The promoter sequence:5′ caaacaattactgctcaatgtatttgcgtatagagcatgtccaataccatgcctcatgatgtgagattgcgaggcggagtcagagaacgagttaaagtgacgacgttttttttgttttttttgggcatagtgtaaagtgatattaaaatttcatggttggcaggtgactgaaaataaaaatgtgtataggatgtgtttatatgctgacggaaaaatagttactcaactaatacagatctttataaagagtatataagtctatggttaatcatgaatggcaatatataagagtagatgagatttatgtttatattgaaacaagggaaagatatgtgtaattgaaacaatggcaaaatataagtcaaatcaaactggtttctgataatatatgtgtttgaatcaatgtatatcttggtattcaaaaccaaaacaactacaccaatttctttaaaaaaccagttgatctaataactacattttaatactagtagctattagctgaatttcataatcaatttcttgcattaaaatttaaagtgggttttgcatttaaacttactcggtttgtattaatagactttcaaagattaaagaaaactactgcattcagagaataaagctatcttactaaacactacttttaaagtttcttttttcacttattaatcttcttttacaaatggatctgtctctctgcatggcaaaatatcttacactaattttattttctttgtttgataacaaatttatcggctaagcatcacttaaatttaatacacgttatgaagacttaaaccacgtcacacTATAagaaccttacaggctgtcaaacacccttccctacccactcacatctctccacgtggcaatctttgatattgacaccttagccactacagctgtcacactcctctctcggtttcaaaacaacatctctggtataaata 3′-aatcaaaacctctcctatatctcttcaatctgatataactacccttctcaATG The promoter wascloned from the organism: Arabidopsis thaliana, WS ecotype Alternativenucleotides: Predicted (Columbia) Experimental (Wassilewskija) PredictedPosition (bp) Mismatch Columbia/Wassilewskija 138 SNP t/— 529 SNP a/t561 SNP a/g 666 Read Error c/c 702 SNP t/a 820 SNP t/a The promoter wascloned in the vector: pNewbin4-HAP1-GFP When cloned into the vector thepromoter was operably linked to a marker, which was the type: GFP-ERPromoter-marker vector was tested in: Arabidopsis thaliana, WS ecotypeGeneration screened:  XT1 Mature XT2 Seedling  T2 Mature  T3 SeedlingThe spatial expression of the promoter-marker vector was found observedin and would be useful in expression in any or all of the following:Flower L anther Ovule Post-fertilization: L endothelium Cotyledon Hepidermis H petiole Rosette Leaf H trichome Primary Root H epidermis Hroot hairs Observed expression pattern of the promoter-marker vector wasin: Expression very weak and may not have been detected by standardscreen. Only tissue with visible GFP expression is analyzed by confocalmicroscopy. This may account for the expressing/screened ratio. T1mature: Low GFP expression in endothelium cells of mature ovules andtapetum cell layer of anthers. Not expressed in pollen. T2 seedling:High GFP expression specific to epidermal tissues of cotyledons, rootand trichomes of rosette leaves. Misc. promoterinformation: Bidirectionality: Exons:   Repeats: The Ceres cDNA ID ofthe endogenous coding sequence to the promoter: 12326995 cDNA nucleotidesequence:aaatcaaaacctctcctatatctcttcaatctgatataactacccttctcaatggcttctaattaccgttttgccatcttcctcactctctttttcgccaccgctggtttctccgccgccgcgttggtcgaggagcagccgcttgttatgaaataccacaacggagttctgttgaaaggtaacatcacagtcaatctcgtatggtacgggaaattcacaccgatccaacggtccgtaatcgtcgatttcatccactcgctaaactccaaagacgttgcatcttccgccgcagttccttccgttgcttcgtggtggaagacgacggagaaatacaaaggtggctcttcaacactcgtcgtcgggaaacagcttctactcgagaactatcctctcggaaaatctctcaaaaatccttacctccgtgctttatccaccaaacttaacggcggtctccgttccataaccgtcgttctaacggcgaaagatgttaccgtcgaaagattctgtatgagccggtgcgggactcacggatcctccggttcgaatccccgtcgcgcagctaacggcgcggcttacgtatgggtcgggaactccgagacgcagtgccctggatattgcgcgtggccgtttcaccagccgatttacggaccacaaacgccgccgttagtagcgcctaacggtgacgttggagttgacggaatgattataaaccttgccacacttctagctaacaccgtgacgaatccgtttaataacggatattaccaaggcccaccaactgcaccgcttgaagctgtgtctgcttgtcctggtatattcgggtcaggttcttatccgggttacgcgggtcgggtacttgttgacaaaacaaccgggtctagttacaacgctcgtggactcgccggtaggaaatatctattgccggcgatgtgggatccgcagagttcgacgtgcaagactctggtttgatccaagggatgtgagtaagacacgtggcatagtagtgagagcgatgacgagatctagacggcatgtgtagtcaaaatcaagttgcacgcgagcgtgtgtataaaaaaatctttcgggtttgggtctcgggtttggattgtggatagggctctctctttgctttttgtcgttttgtaatgacgtgtaaaaactgtactcggaaatgtgaagaatgcatataaaataataaaaaatcattttgtttctact Coding sequence:MASNYRFAIFLTLFFATAGFSAAALVEEQPLVMKYHNGVLLKGNITVNLVWYGKFTPIQRSVIVDFIHSLNSKDVASSAAVPSVASWWKTTEKYKGGSSTLVVGKQLLLENYPLGKSLKNPYLRALSTKLNGGLRSITVVLTAKDVTVERFCMSRCGTHGSSGSNPRRAANGAAYVWVGNSETQCPGYCAWPFHQPIYGPQTPPLVAPNGDVGVDGMIINLATLLANTVTNPFNNGYYQGPPTAPLEAVSACPGIFGSGSYPGYAGRVLVDKTTGSSYNARGLAGRKYLLPAMWDPQSSTCKTLV* Microarray data shows thatthe coding sequence was expressed in the following experiments, whichshows that the promoter would be useful to modulate expression insituations similar to the following: CDNA_ID SHORT_NAME EXPT_REP_IDIS_UP 12326995 At_Root_Tips 108434 − 12326995 At_Germinating_Seeds108462 + 12326995 At_Germinating_Seeds 108463 + 12326995 At_42deg_Heat108576 + 12326995 At_100 uM_ABA_Mutants 20000072 + 12326995At_42deg_Heat 20000111 + 12326995 At_42deg_Heat 20000144 + 12326995At_100 uM_ABA 20000166 + 12326995 At_100 uM_ABA 20000169 + 12326995At_2mM_SA 20000181 + 12326995 At_Siliques 20000234 − 12326995At_Siliques 20000235 − 12326995 At_Siliques 20000236 − 12326995At_Open_Flower 20000265 − 12326995 At_Open_Flower 20000286 − 12326995At_Pollen 20000326 − 12326995 At_100 uM_ABA 20000453 + 12326995At_Far-red-induction 20001247 + 12326995 At_Far-red-induction 20001248 +12326995 At_Far-red-induction 20001450 + 12326995 At_Far-red-induction20001451 + 12326995 At_Drought_Soil_Dry 20001556 − 12326995At_Drought_Soil_Dry 20001557 − 12326995 At_Drought_Soil_Dry 20001558 −12326995 At_Interploidy_Crosses 20001654 + 12326995At_Drought_Reproduction 20001904 − 12326995 At_8deg_Cold 20002103 −12326995 At_8deg_Cold 20002105 − Microarray data shows that the codingsequence was expressed in the following experiments, which shows thatthe promoter would be useful to modulate expression in situationssimilar to the following: CDNA_ID SHORT_NAME EXPT_REP_ID PARAM_NAMEVALUE 12326995 At_Root_Tips 108434 Tissue Root Tips 12326995At_Germinating_Seeds 108462 Age (day) 2 vs. 0 12326995At_Germinating_Seeds 108462 Tissue Germinating Seeds 12326995At_Germinating_Seeds 108463 Age (day) 3 vs. 0 12326995At_Germinating_Seeds 108463 Tissue Germinating Seeds 12326995At_42deg_Heat 108576 Timepoint (hr) 1 12326995 At_42deg_Heat 108576Temperature (deg C.) 42 vs. 22 12326995 At_42deg_Heat 108576 TissueAerial 12326995 At_100 uM_ABA_Mutants 20000072 Timepoint (hr) 6 12326995At_100 uM_ABA_Mutants 20000072 Treatment 100 uM ABA vs. No Treatment12326995 At_100 uM_ABA_Mutants 20000072 Tissue Aerial 12326995 At_100uM_ABA_Mutants 20000072 Plant Line CS8105 12326995 At_42deg_Heat20000111 Timepoint (hr) 6 12326995 At_42deg_Heat 20000111 Temperature(deg C.) 42 vs. 22 12326995 At_42deg_Heat 20000111 Tissue Aerial12326995 At_42deg_Heat 20000144 Timepoint (hr) 1 12326995 At_42deg_Heat20000144 Temperature (deg C.) 42 vs. 22 12326995 At_42deg_Heat 20000144Tissue Aerial 12326995 At_100 uM_ABA 20000166 Timepoint (hr) 1 12326995At_100 uM_ABA 20000166 Age (day) 14 12326995 At_100 uM_ABA 20000166Treatment 100 uM ABA vs. No Treatment 12326995 At_100 uM_ABA 20000166Organism A. thaliana 12326995 At_100 uM_ABA 20000166 Tissue Aerial12326995 At_100 uM_ABA 20000166 Plant Line WS 12326995 At_100 uM_ABA20000169 Timepoint (hr) 6 12326995 At_100 uM_ABA 20000169 Age (day) 1412326995 At_100 uM_ABA 20000169 Treatment 100 uM ABA vs. No Treatment12326995 At_100 uM_ABA 20000169 Organism A. thaliana 12326995 At_100uM_ABA 20000169 Tissue Aerial 12326995 At_100 uM_ABA 20000169 Plant LineWS 12326995 At_2mM_SA 20000181 Timepoint (hr) 1 12326995 At_2mM_SA20000181 Age (day) 14 12326995 At_2mM_SA 20000181 Treatment 2 mM SA vs.No Treatment 12326995 At_2mM_SA 20000181 Organism A. thaliana 12326995At_2mM_SA 20000181 Tissue Aerial 12326995 At_2mM_SA 20000181 Plant LineWS 12326995 At_Siliques 20000234 Age (day) 21 12326995 At_Siliques20000234 Tissue <5 mm Siliques vs. Whole Plant 12326995 At_Siliques20000234 Organism A. thaliana 12326995 At_Siliques 20000234 Plant LineWS 12326995 At_Siliques 20000235 Age (day) 21 12326995 At_Siliques20000235 Tissue 5-10 mm Siliques vs. Whole Plant 12326995 At_Siliques20000235 Organism A. thaliana 12326995 At_Siliques 20000235 Plant LineWS 12326995 At_Siliques 20000236 Age (day) 21 12326995 At_Siliques20000236 Tissue >10 mm Siliques vs. Whole Plant 12326995 At_Siliques20000236 Organism A. thaliana 12326995 At_Siliques 20000236 Plant LineWS 12326995 At_Open_Flower 20000265 Age (day) 21 12326995 At_Open_Flower20000265 Organism A. thaliana 12326995 At_Open_Flower 20000265 TissueClosed Flower vs. Whole Plant 12326995 At_Open_Flower 20000265 PlantLine WS 12326995 At_Open_Flower 20000286 Age (day) 21 12326995At_Open_Flower 20000286 Organism A. thaliana 12326995 At_Open_Flower20000286 Tissue Half Open vs. Whole Plant 12326995 At_Open_Flower20000286 Plant Line WS 12326995 At_Pollen 20000326 Age (day) 0 vs. 2112326995 At_Pollen 20000326 Organism A. thaliana 12326995 At_Pollen20000326 Tissue Pollen vs. Whole Plant 12326995 At_Pollen 20000326 PlantLine WS 12326995 At_100 uM_ABA 20000453 Age (day) 15 12326995 At_100uM_ABA 20000453 Timepoint (hr) 24 12326995 At_100 uM_ABA 20000453Treatment 100 uM ABA vs. No Treatment 12326995 At_100 uM_ABA 20000453Organism A. thaliana 12326995 At_100 uM_ABA 20000453 Tissue Aerial12326995 At_100 uM_ABA 20000453 Plant Line WS 12326995At_Far-red-induction 20001247 Timepoint (hr) 1 12326995At_Far-red-induction 20001247 Age (day) 7 12326995 At_Far-red-induction20001247 Organism A. thaliana 12326995 At_Far-red-induction 20001247Plant Line Columbia 12326995 At_Far-red-induction 20001247 Light Far-redvs. White 12326995 At_Far-red-induction 20001247 Tissue Whole Plant12326995 At_Far-red-induction 20001248 Timepoint (hr) 4 12326995At_Far-red-induction 20001248 Age (day) 7 12326995 At_Far-red-induction20001248 Organism A. thaliana 12326995 At_Far-red-induction 20001248Plant Line Columbia 12326995 At_Far-red-induction 20001248 Light Far-redvs. White 12326995 At_Far-red-induction 20001248 Tissue Whole Plant12326995 At_Far-red-induction 20001450 Age (day) 7 12326995At_Far-red-induction 20001450 Timepoint (hr) 8 12326995At_Far-red-induction 20001450 Organism A. thaliana 12326995At_Far-red-induction 20001450 Plant Line Columbia 12326995At_Far-red-induction 20001450 Light Far-red vs. White 12326995At_Far-red-induction 20001450 Tissue Whole Plant 12326995At_Far-red-induction 20001451 Age (day) 8 12326995 At_Far-red-induction20001451 Timepoint (hr) 24 12326995 At_Far-red-induction 20001451Organism A. thaliana 12326995 At_Far-red-induction 20001451 Plant LineColumbia 12326995 At_Far-red-induction 20001451 Light Far-red vs. White12326995 At_Far-red-induction 20001451 Tissue Whole Plant 12326995At_Drought_Soil_Dry 20001556 Timepoint (day) 12 12326995At_Drought_Soil_Dry 20001556 Age (day) 26 12326995 At_Drought_Soil_Dry20001556 Organism A. thaliana 12326995 At_Drought_Soil_Dry 20001556Treatment Drought vs. No Drought 12326995 At_Drought_Soil_Dry 20001556Post Timepoint (hr) None 12326995 At_Drought_Soil_Dry 20001556Post-Treatment None 12326995 At_Drought_Soil_Dry 20001556 Plant Line WS12326995 At_Drought_Soil_Dry 20001557 Post Timepoint (hr) 3 12326995At_Drought_Soil_Dry 20001557 Timepoint (day) 13 12326995At_Drought_Soil_Dry 20001557 Age (day) 27 12326995 At_Drought_Soil_Dry20001557 Organism A. thaliana 12326995 At_Drought_Soil_Dry 20001557Treatment Drought vs. No Drought 12326995 At_Drought_Soil_Dry 20001557Post-Treatment Re-Water vs. No Drought 12326995 At_Drought_Soil_Dry20001557 Plant Line WS 12326995 At_Drought_Soil_Dry 20001558 PostTimepoint (hr) 6 12326995 At_Drought_Soil_Dry 20001558 Timepoint (day)13 12326995 At_Drought_Soil_Dry 20001558 Age (day) 27 12326995At_Drought_Soil_Dry 20001558 Organism A. thaliana 12326995At_Drought_Soil_Dry 20001558 Treatment Drought vs. No Drought 12326995At_Drought_Soil_Dry 20001558 Post-Treatment Re-Water vs. No Drought12326995 At_Drought_Soil_Dry 20001558 Plant Line WS 12326995At_Interploidy_Crosses 20001654 Age (day) 5 12326995At_Interploidy_Crosses 20001654 Cross 6X × 2X vs. 2X × 2X 12326995At_Interploidy_Crosses 20001654 Organism A. thaliana 12326995At_Interploidy_Crosses 20001654 Plant Line Columbia 12326995At_Interploidy_Crosses 20001654 Tissue Siliques 12326995At_Drought_Reproduction 20001904 Timepoint (day) 7 12326995At_Drought_Reproduction 20001904 Age (day) 37 12326995At_Drought_Reproduction 20001904 Organism A. thaliana 12326995At_Drought_Reproduction 20001904 Treatment Drought vs. No Drought12326995 At_Drought_Reproduction 20001904 Tissue Rosettes 12326995At_Drought_Reproduction 20001904 Plant Line WS 12326995 At_8deg_Cold20002103 Timepoint (hr) 2 12326995 At_8deg_Cold 20002103 Age (day) 712326995 At_8deg_Cold 20002103 Temperature (deg C.) 8 vs. 22 12326995At_8deg_Cold 20002103 Organism A. thaliana 12326995 At_8deg_Cold20002103 Tissue Whole Plant 12326995 At_8deg_Cold 20002103 Plant Line WS12326995 At_8deg_Cold 20002105 Age (day) 7 12326995 At_8deg_Cold20002105 Timepoint (hr) 8 12326995 At_8deg_Cold 20002105 Temperature(deg C.) 8 vs. 22 12326995 At_8deg_Cold 20002105 Organism A. thaliana12326995 At_8deg_Cold 20002105 Tissue Whole Plant 12326995 At_8deg_Cold20002105 Plant Line WS Promoter YP0286 Modulates the gene: Hypotheticalprotein The GenBank description of the gene: NM_102758 Arabidopsisthaliana hypothetical protein (At1g30190) mRNA, complete cdsgi|18397396|ref|NM_102758.1|[18397396] The promoter sequence:5′atcatcgaaaggtatgtgatgcatattcccattgaaccagatttccatatattttatttgtaaagtgataatgaatcacaagatgattcaatattaaaaatgggtaactcactttgacgtgtagtacgtggaagaatagttagctatcacgcatatatatatctatgattaagtgtgtatgacataagaaactaaaatatttacctaaagtccagttactcatactgattttatgcatatatgtattatttatttatttttaataaagaagcgattggtgttttcatagaaatcatgatagattgataggtatttcagttccacaaatctagatctgtgtgctatacatgcatgtattaattttttccccttaaatcatttcagttgataatattgctctttgttccaactttagaaaaggtatgaaccaacctgacgattaacaagtaaacattaattaatctttatatatatgagataaaaccgaggatatatatgattgtgttgctgtctattgatgatgtgtcgatattatgcttgttgtaccaatgctcgagccgagcgtgatcgatgccttgacaaactatatatgtttcccgaattaattaagttttgtatcttaattagaataacatttttatacaatgtaatttctcaagcagacaagatatgtatcctatattaattactatatatgaattgccgggcacctaccaggatgtttcaaatacgagagcccattagtttccacgtaaatcacaatgacgcgacaaaatctagaatcgtgtcaaaactctatcaatacaataatatatatttcaagggcaatttcgacttctcctcaactcaatgattcaacgccatgaatctctaTATAaaggctacaacaccacaaaggatcatcagtcatcacaaccacattaactcttcaccactatctctcaatctct 3′-ATG The promoter was cloned from theorganism: Arabidopsis thaliana, WS ecotype Alternative nucleotides:Predicred (Columbia) Experimental (Wassilewskija) Predicted Position(bp) Mismatch Columbia/Wassilewskija 194 SNP t/a 257 SNP t/c 491-494SSLP tata/— — — — 527 No g in Ws —/— The promoter was cloned in thevector: pNewbin4-HAP1-GFP When cloned into the vector the promoter wasoperably linked to a marker, which was the type: GFP-ER Promoter-markervector was tested in: Arabidopsis thaliana, WS ecotype Generationscreened: XT1 Mature   XT2 Seedling   T2 Mature   T3 Seedling Thespatial expression of the promoter-marker vector was found observed inand would be useful in expression in any or all of the following: FlowerL pedicel L epidermis Stem L epidermis Hypocotyl H epidermis Cotyledon Hmesophyll H vascular H epidermis H petiole Rosette Leaf H epidermis Hpetiole Primary Root H epidermis Lateral root H lateral root capObserved expression pattern of the promoter-marker vector was in: T1mature: GFP expressed in vasculature of silique and pedicles of flowers.T2 seedling: High GFP expression throughout vasculature of root,hypocotyl, and petioles. Misc. promoter information:  Bidirectionality:Pass  Exons: Pass   Repeats: No The Ceres cDNA ID of the endogenouscoding sequence to the promoter: 12669548 cDNA nucleotide sequence:ATGACAGAAATGCCCTCGTACATGATCGAGAACCCAAAGTTCGAGCCAAAGAAACGACGTTATTACTCTTCTTCGATGCTTACCATCTTCTTACCGATCTTCACATACATTATGATCTTTCACGTTTTCGAAGTATCACTATCTTCGGTCTTTAAAGACACAAAGGTCTTGTTCTTCATCTCCAATACTCTCATCCTCATAATAGCCGCCGATTATGGTTCCTTCTCTGATAAAGAGAGTCAAGACTTTTACGGTGAATACACTGTCGCAGCGGCAACGATGCGAAACCGAGCTGATAACTACTCTCCGATTCCCGTCTTGACATACCGAGAAAACACTAAAGATGGAGAAATCAAGAACCCTAAAGATGTCGAATTCAGGAACCCTGAAGAAGAAGACGAACCGATGGTGAAAGATATCATTTGCGTTTCTCCTCCCGAGAAAATAGTACGAGTGGTGAGTGAGAAGAAACAGAGAGATGATGTAGCTATGGAAGAATACAAACCAGTTACAGAACAAACTCTTGCTAGCGAAGAAGCTTGCAACACAAGAAACCATGTGAACCCTAATAAACCGTACGGGCGAAGTAAATCAGATAAGCCACGGAGAAAGAGGCTCAGCGTAGATACAGAGACGACCAAACGTAAAAGTTATGGTCGAAAGAAATCAGATTGCTCGAGATGGATGGTTATTCCGGAGAAGTGGGAATATGTTAAAGAAGAATCTGAAGAGTTTTCAAAGTTGTCCAACGAGGAGTTGAACAAACGAGTCGAAGAATTCATCCAACGGTTCAATAGACAGATCAGATCACAATCACCGCGAGTTTCGTCTACTTGA Coding sequence:MTEMPSYMIENPKFEPKKRRYYSSSMLTIFLPIFTYIMIFHVFEVSLSSVFKDTKVLFFISNTLILIIAADYGSFSDKESQDFYGEYTVAAATMRNRADNYSPIPVLTYRENTKDGEIKNPKDVEFRNPEEEDEPMVKDIICVSPPEKIVRVVSEKKQRDDVAMEEYKPVTEQTLASEEACNTRNHVNPNKPYGRSKSDKPRRKRLSVDTETTKRKSYGRKKSDCSRWMVIPEKWEYVKEESEEFSKLSNEELNKRVEEFIQRFNRQIRSQSPRVSST* Microarray data shows that thecoding sequence was expressed in the following experiments, which showsthat the promoter would be useful to modulate expression in situationssimilar to the following: CDNA_ID SHORT_NAME EXPT_REP_ID IS_UP 12669548At_100uM_ABA 20000169 + 12669548 At_42deg_Heat 20000171 + 12669548At_42deg_Heat 20000173 + 12669548 At_2mM_SA 20000182 + 12669548At_0.001_percent_MeJA 20000211 − 12669548 At_Open_Flower 20000264 −12669548 At_Open_Flower 20000265 − 12669548 At_Drought 20000267 +12669548 At_100mM_NaCl 20000268 + 12669548 At_Open_Flower 20000286 −12669548 At_Drought 20000436 + 12669548 At_Drought 20000437 + 12669548At_100uM_NAA 20000444 + 12669548 At_100uM_NAA 20000445 + 12669548At_100uM_ABA 20000453 + 12669548 At_42deg_Heat 20000457 − 12669548At_10percent_PEG 20000527 + 12669548 At_Line_Comparisons 20001192 −12669548 At_Line_Comparisons 20001307 + 12669548 At_Line_Comparisons20001309 − 12669548 At_Line_Comparisons 20001310 − 12669548At_Drought_Soil_Dry 20001554 + 12669548 At_Drought_Soil_Dry 20001555 +12669548 At_Drought_Soil_Dry 20001556 + 12669548 At_Drought_Soil_Dry20001559 + 12669548 At_50mM_NH4NO3_L-to-H 20001757 − 12669548At_Drought_Reproduction 20001904 + 12669548 At_Drought_Reproduction20001905 + 12669548 At_Drought_Reproduction 20001910 + 12669548At_Drought_Reproduction 20001911 + 12669548 At_Line_Comparisons20002009 + 12669548 At_Line_Comparisons 20002010 + 12669548At_Drought-Air-Dry 20002253 − 12669548 At_Drought-Air-Dry 20002256 + Theparameters for the microarray experiments listed above by Expt_Rep_IDand Short_Name are as follow below: CDNA_ID SHORT_NAME EXPT_REP_IDPARAM_NAME VALUE 12669548 At_100uM_ABA 20000169 Timepoint (hr) 612669548 At_100uM_ABA 20000169 Age (day) 14 12669548 At_100uM_ABA20000169 Treatment 100 uM ABA vs. No Treatment 12669548 At_100uM_ABA20000169 Organism A. thaliana 12669548 At_100uM_ABA 20000169 TissueAerial 12669548 At_100uM_ABA 20000169 Plant Line WS 12669548At_42deg_Heat 20000171 Timepoint (hr) 1 12669548 At_42deg_Heat 20000171Age (day) 14 12669548 At_42deg_Heat 20000171 Temperature (deg C.) 42 vs.22 12669548 At_42deg_Heat 20000171 Organism A. thaliana 12669548At_42deg_Heat 20000171 Tissue Aerial 12669548 At_42deg_Heat 20000171Plant Line WS 12669548 At_42deg_Heat 20000173 Timepoint (hr) 6 12669548At_42deg_Heat 20000173 Age (day) 14 12669548 At_42deg_Heat 20000173Temperature (deg C.) 42 vs. 22 12669548 At_42deg_Heat 20000173 OrganismA. thaliana 12669548 At_42deg_Heat 20000173 Tissue Aerial 12669548At_42deg_Heat 20000173 Plant Line WS 12669548 At_2mM_SA 20000182Timepoint (hr) 6 12669548 At_2mM_SA 20000182 Age (day) 14 12669548At_2mM_SA 20000182 Treatment 2 mM SA vs. No Treatment 12669548 At_2mM_SA20000182 Organism A. thaliana 12669548 At_2mM_SA 20000182 Tissue Aerial12669548 At_2mM_SA 20000182 Plant Line WS 12669548 At_0.001percent_MeJA20000211 Timepoint (hr) 1 12669548 At_0.001percent_MeJA 20000211 Age(day) 14 12669548 At_0.001percent_MeJA 20000211 Treatment 0.001 percentMeJA vs. No Treatment 12669548 At_0.001percent_MeJA 20000211 Organism A.thaliana 12669548 At_0.001percent_MeJA 20000211 Tissue Aerial 12669548At_0.001percent_MeJA 20000211 Plant Line WS 12669548 At_Open_Flower20000264 Age (day) 21 12669548 At_Open_Flower 20000264 Organism A.thaliana 12669548 At_Open_Flower 20000264 Tissue Open Flower vs. WholePlant 12669548 At_Open_Flower 20000264 Plant Line WS 12669548At_Open_Flower 20000265 Age (day) 21 12669548 At_Open_Flower 20000265Organism A. thaliana 12669548 At_Open_Flower 20000265 Tissue ClosedFlower vs. Whole Plant 12669548 At_Open_Flower 20000265 Plant Line WS12669548 At_Drought 20000267 Timepoint (hr) 6 12669548 At_Drought20000267 Age (day) 7 12669548 At_Drought 20000267 Organism A. thaliana12669548 At_Drought 20000267 Treatment Drought vs. No Drought 12669548At_Drought 20000267 Tissue Whole Plant 12669548 At_Drought 20000267Plant Line WS 12669548 At_100mM_NaCl 20000268 Timepoint (hr) 6 12669548At_100mM_NaCl 20000268 Age (day) 14 12669548 At_100mM_NaCl 20000268Treatment 100 mM NaCl vs. No Treatment 12669548 At_100mM_NaCl 20000268Organism A. thaliana 12669548 At_100mM_NaCl 20000268 Tissue Whole Plant12669548 At_100mM_NaCl 20000268 Plant Line WS 12669548 At_Open_Flower20000286 Age (day) 21 12669548 At_Open_Flower 20000286 Organism A.thaliana 12669548 At_Open_Flower 20000286 Tissue Half Open vs. WholePlant 12669548 At_Open_Flower 20000286 Plant Line WS 12669548 At_Drought20000436 Age (day) 7 12669548 At_Drought 20000436 Timepoint (hr) 1212669548 At_Drought 20000436 Organism A. thaliana 12669548 At_Drought20000436 Treatment Drought vs. No Drought 12669548 At_Drought 20000436Tissue Whole Plant 12669548 At_Drought 20000436 Plant Line WS 12669548At_Drought 20000437 Age (day) 8 12669548 At_Drought 20000437 Timepoint(hr) 24 12669548 At_Drought 20000437 Organism A. thaliana 12669548At_Drought 20000437 Treatment Drought vs. No Drought 12669548 At_Drought20000437 Tissue Whole Plant 12669548 At_Drought 20000437 Plant Line WS12669548 At_100uM_NAA 20000444 Timepoint (hr) 1 12669548 At_100uM_NAA20000444 Age (day) 14 12669548 At_100uM_NAA 20000444 Treatment 100 uMNAA vs. No Treatment 12669548 At_100uM_NAA 20000444 Organism A. thaliana12669548 At_100uM_NAA 20000444 Tissue Aerial 12669548 At_100uM_NAA20000444 Plant Line WS 12669548 At_100uM_NAA 20000445 Timepoint (hr) 612669548 At_100uM_NAA 20000445 Age (day) 14 12669548 At_100uM_NAA20000445 Treatment 100 uM NAA vs. No Treatment 12669548 At_100uM_NAA20000445 Organism A. thaliana 12669548 At_100uM_NAA 20000445 TissueAerial 12669548 At_100uM_NAA 20000445 Plant Line WS 12669548At_100uM_ABA 20000453 Age (day) 15 12669548 At 100uM_ABA 20000453Timepoint (hr) 24 12669548 At_100uM_ABA 20000453 Treatment 100 uM ABAvs. No Treatment 12669548 At_100uM_ABA 20000453 Organism A. thaliana12669548 At_100uM_ABA 20000453 Tissue Aerial 12669548 At_100uM_ABA20000453 Plant Line WS 12669548 At_42deg_Heat 20000457 Timepoint (hr)0.166 12669548 At_42deg_Heat 20000457 Age (day) 14 12669548At_42deg_Heat 20000457 Temperature (deg C.) 42 vs. 22 12669548At_42deg_Heat 20000457 Organism A. thaliana 12669548 At_42deg_Heat20000457 Tissue Aerial 12669548 At_42deg_Heat 20000457 Plant Line WS12669548 At_10percent_PEG 20000527 Age (day) 20 12669548At_10percent_PEG 20000527 Timepoint (day) 20 12669548 At_10percent_PEG20000527 Treatment 10 percent PEG vs. No Treatment 12669548At_10percent_PEG 20000527 Organism A. thaliana 12669548 At_10percent_PEG20000527 Tissue Whole Plant 12669548 At_10percent_PEG 20000527 PlantLine WS 12669548 At_Line_Comparisons 20001192 Plant Line WBin4-WX13R-Avs. WS 12669548 At_Line_Comparisons 20001307 Plant Line WBin4-WX2-A vs.WS 12669548 At_Line_Comparisons 20001309 Plant Line WBin4-WX49R-A vs. WS12669548 At_Line_Comparisons 20001310 Plant Line WBin4-WX17-A vs. WS12669548 At_Drought_Soil_Dry 20001554 Timepoint (day) 7 12669548At_Drought_Soil_Dry 20001554 Age (day) 21 12669548 At_Drought_Soil_Dry20001554 Organism A. thaliana 12669548 At_Drought_Soil_Dry 20001554Treatment Drought vs. No Drought 12669548 At_Drought_Soil_Dry 20001554Post Timepoint (hr) None 12669548 At_Drought_Soil_Dry 20001554Post-Treatment None 12669548 At_Drought_Soil_Dry 20001554 Plant Line WS12669548 At_Drought_Soil_Dry 20001555 Timepoint (day) 10 12669548At_Drought_Soil_Dry 20001555 Age (day) 24 12669548 At_Drought_Soil_Dry20001555 Organism A. thaliana 12669548 At_Drought_Soil_Dry 20001555Treatment Drought vs. No Drought 12669548 At_Drought_Soil_Dry 20001555Post Timepoint (hr) None 12669548 At_Drought_Soil_Dry 20001555Post-Treatment None 12669548 At_Drought_Soil_Dry 20001555 Plant Line WS12669548 At_Drought_Soil_Dry 20001556 Timepoint (day) 12 12669548At_Drought_Soil_Dry 20001556 Age (day) 26 12669548 At_Drought_Soil_Dry20001556 Organism A. thaliana 12669548 At_Drought_Soil_Dry 20001556Treatment Drought vs. No Drought 12669548 At_Drought_Soil_Dry 20001556Post Timepoint (hr) None 12669548 At_Drought_Soil_Dry 20001556Post-Treatment None 12669548 At_Drought_Soil_Dry 20001556 Plant Line WS12669548 At_Drought_Soil_Dry 20001559 Timepoint (day) 14 12669548At_Drought_Soil_Dry 20001559 Age (day) 28 12669548 At_Drought_Soil_Dry20001559 Post Timepoint (hr) 29 12669548 At_Drought_Soil_Dry 20001559Organism A. thaliana 12669548 At_Drought_Soil_Dry 20001559 TreatmentDrought vs. No Drought 12669548 At_Drought_Soil_Dry 20001559Post-Treatment Re-Water vs. No Drought 12669548 At_Drought_Soil_Dry20001559 Plant Line WS 12669548 At_50mM_NH4NO3_L-to-H 20001757 Timepoint(hr) 6 12669548 At_50mM_NH4NO3_L-to-H 20001757 Treatment 50 mM NH4NO3 vs100 mM Mannitol 12669548 At_50mM_NH4NO3_L-to-H 20001757 Tissue Leaf12669548 At_Drought_Reproduction 20001904 Timepoint (day) 7 12669548At_Drought_Reproduction 20001904 Age (day) 37 12669548At_Drought_Reproduction 20001904 Organism A. thaliana 12669548At_Drought_Reproduction 20001904 Treatment Drought vs. No Drought12669548 At_Drought_Reproduction 20001904 Tissue Rosettes 12669548At_Drought_Reproduction 20001904 Plant Line WS 12669548At_Drought_Reproduction 20001905 Timepoint (day) 10 12669548At_Drought_Reproduction 20001905 Age (day) 40 12669548At_Drought_Reproduction 20001905 Organism A. thaliana 12669548At_Drought_Reproduction 20001905 Treatment Drought vs. No Drought12669548 At_Drought_Reproduction 20001905 Tissue Rosettes 12669548At_Drought_Reproduction 20001905 Plant Line WS 12669548At_Drought_Reproduction 20001910 Timepoint (day) 7 12669548At_Drought_Reproduction 20001910 Age (day) 37 12669548At_Drought_Reproduction 20001910 Organism A. thaliana 12669548At_Drought_Reproduction 20001910 Treatment Drought vs. No Drought12669548 At_Drought_Reproduction 20001910 Tissue Flowers 12669548At_Drought_Reproduction 20001910 Plant Line WS 12669548At_Drought_Reproduction 20001911 Timepoint (day) 10 12669548At_Drought_Reproduction 20001911 Age (day) 40 12669548At_Drought_Reproduction 20001911 Organism A. thaliana 12669548At_Drought_Reproduction 20001911 Treatment Drought vs. No Drought12669548 At_Drought_Reproduction 20001911 Tissue Flowers 12669548At_Drought_Reproduction 20001911 Plant Line WS 12669548At_Line_Comparisons 20002009 Plant Line ME01642 vs. WS 12669548At_Line_Comparisons 20002010 Plant Line ME02031 vs. WS 12669548At_Drought-Air-Dry 20002253 Timepoint (hr) 1 12669548 At_Drought-Air-Dry20002253 Age (day) 35 12669548 At_Drought-Air-Dry 20002253 Organism A.thaliana 12669548 At_Drought-Air-Dry 20002253 Treatment Drought vs. NoDrought 12669548 At_Drought-Air-Dry 20002253 Tissue Roots 12669548At_Drought-Air-Dry 20002253 Plant Line WS 12669548 At_Drought-Air-Dry20002256 Timepoint (hr) 4 12669548 At_Drought-Air-Dry 20002256 Age (day)35 12669548 At_Drought-Air-Dry 20002256 Organism A. thaliana 12669548At_Drought-Air-Dry 20002256 Treatment Drought vs. No Drought 12669548At_Drought-Air-Dry 20002256 Tissue Shoots 12669548 At_Drought-Air-Dry20002256 Plant Line WS Promoter YP0275 Modulates the gene: Glycosylhydrolase family. The GenBank description of the gene: NM_115876Arabidopsis thaliana glycosyl hydrolase family 1 (At3g60130) mRNA,complete cds gi|30695130|ref|NM_115876.2|[30695130] The promotersequence:5′gcgtatgctttactttttaaaatgggcctatgctataattgaatgacaaggattaaacaactaataaaagtgtagatgggttaagatgacttatttttttacttaccaatttataaatgggcttcgatgtactgaaatatatcgcgcctattaacgaggccattcaacgaatgttttaagggccctatttcgacattttaaagaacacctaggtcatcattccagaaatggatattataggatttagataatttcccacgtttggtttatttatctattttttgacgttgaccaacataatcgtgcccaaccgtttcacgcaacgaatttatatacgaaatatatatatttttcaaattaagataccacaatcaaaacagctgttgattaacaaagagattttttttttttggttttgagttacaataacgttagaggataaggtttcttgcaacgattaggaaatcgtataaaataaaatatgttataattaagtgttttattttataatgagtattaatataaataaaacctgcaaaaggatagggatattgaataataaagagaaacgaaagagcaattttacttctttataattgaaattatgtgaatgttatgtttacaatgaatgattcatcgttctatatattgaagtaaagaatgagtttattgtgcttgcataatgacgttaacttcacatatacacttattacataacatttatcacatgtgcgtctttttttttttttactttgtaaaatttcctcactttaaagacttttataacaattactagtaaaataaagttgcttggggctacaccctttctccctccaacaactctatttatagataacattatatcaaaatcaaaacatagtccctttcttctataaaggttttttcacaaccaaatttccarTATAaatcaaaaaataaaaacttaatta 3′-aATG The promoter was cloned from theorganism: Arabidopsis thaliana, WS ecotype Alternative nucleotides:Predicted (Columbia) Experimenral (Wassilewskija) Sequence (bp) MismatchColumbia/Wassilewskija  95 SNP g/t 798 SNP a/t The promoter was clonedin the vector: pNewbin4-HAP1-GFP When cloned into the vector thepromoter was operably linked to a marker, which was the type: GFP-ERPromoter-marker vector was tested in: Arabidopsis thaliana, WS ecotypeGeneration screened: XT1 Mature   XT2 Seedling   T2 Mature   T3 SeedlingThe spatial expression of the promoter-marker vector was found observedin and would be useful in expression in any or all of the following:Primary Root H epidermis H trichoblast H atrichoblast L root cap H roothairs Observed expression pattern of the promoter-marker vector was in:T1 mature: No expression. T2 seedling: High expression in root epidermalat transition zone decreasing toward root tip. Misc. promoterinformation:  Bidirectionality: Pass  Exons: Pass   Repeats: No TheCeres cDNA ID of the endogenous coding sequence to the promoter:12668112 cDNA nucleotide sequence:ATAAAAACTTAATTAGTTTTTACAGAAGAAAAGAAAACAATGAGAGGTAAATTTCTAAGTTTACTGTTGCTCATTACTTTGGCCTGCATTGGAGTTTCCGCCAAGAAGCATTCCACAAGGCCTAGATTAAGAAGAAATGATTTCCCACAAGATTTCGTTTTTGGATCTGCTACTTCTGCTTATCAGTGTGAAGGAGCTGCACATGAAGATGGTAGAGGTCCAAGTATCTGGGACTCCTTCTCTGAAAAATTCCCAGAAAAGATAATGGATGGTAGTAATGGGTCCATTGCAGATGATTCTTACAATCTTTACAAGGAAGATGTGAATTTGCTGCATCAAATTGGCTTCGATGCTTACCGATTTTCGATCTCATGGTCACGGATTTTGCCTCGTGGGACTCTAAAGGGAGGAATCAACCAGGCTGGAATTGAATATTATAACAACTTGATTAATCAACTTATATCTAAAGGAGTGAAGCCATTTGTCACACTCTTTCACTGGGACTTACCAGATGCACTCGAAAATGCTTACGGTGGCCTCCTTGGAGATGAATTTGTGAACGATTTCCGAGACTATGCAGAACTTTGTTTCCAGAAGTTTGGAGATAGAGTGAAGCAGTGGACGACACTAAACGAGCCATATACAATGGTACATGAAGGTTATATAACAGGTCAAAAGGCACCTGGAAGATGTTCCAATTTCTATAAACCTGATTGCTTAGGTGGCGATGCAGCCACGGAGCCTTACATCGTCGGCCATAACCTCCTCCTTGCTCATGGAGTTGCCGTAAAAGTATATAGAGAAAAGTACCAGGCAACTCAGAAAGGTGAAATTGGTATTGCCTTAAACACAGCATGGCACTACCCTTATTCAGATTCATATGCTGACCGGTTAGCTGCGACTCGAGCGACTGCCTTCACCTTCGACTACTTCATGGAGCCAATCGTGTACGGTAGATATCCAATTGAAATGGTCAGCCACGTTAAAGACGGTCGTCTTCCTACCTTCACACCAGAAGAGTCCGAAATGCTCAAAGGATCATATGATTTCATAGGCGTTAACTATTACTCATCTCTTTACGCAAAAGACGTGCCGTGTGCAACTGAAAACATCACCATGACCACCGATTCTTGCGTCAGCCTCGTAGGTGAACGAAATGGAGTGCCTATCGGTCCAGCGGCTGGATCGGATTGGCTTTTGATATATCCCAAGGGTATTCGTGATCTCCTACTACATGCAAAATTCAGATACAATGATCCCGTCTTGTACATTACAGAGAATGGAGTGGATGAAGCAAATATTGGCAAAATATTTCTTAACGACGATTTGAGAATTGATTACTATGCTCATCACCTCAAGATGGTTAGCGATGCTATCTCGATCGGGGTGAATGTGAAGGGATATTTCGCGTGGTCATTGATGGATAATTTCGAGTGGTCGGAAGGATACACGGTCCGGTTCGGGCTAGTGTTTGTGGACTTTGAAGATGGACGTAAGAGGTATCTGAAGAAATCAGCTAAGTGGTTTAGGAGATTGTTGAAGGGAGCGCATGGTGGGACGAATGAGCAGGTGGCTGTTATTTAATAAACCACGAGTCATTGGTCAATTTAGTCTACTGTTTCTTTTGCTCTATGTACAGAAAGAAAATAAACTTTCCAAAATAAGAGGTGGCTTTGTTTGGACTTTGGATGTTACTATATATATTGGTAATTCTTGGCGTTTGTTAGTTTCCAAACCAAACATTAAT Coding sequence:MRGKFLSLLLLITLACIGVSAKKHSTRPRLRRNDFPQDFVFGSATSAYQCEGAAHEDGRGPSIWDSFSEKFPEKIMDGSNGSIADDSYNLYKEDVNLLHQIGFDAYRFSISWSRILPRGTLKGGINQAGIEYYNNLINQLISKGVKPFVTLFHWDLPDALENAYGGLLGDEFVNDFRDYAELCFQKFGDRVKQWTTLNEPYTMVHEGYITGQKAPGRCSNFYKPDCLGGDAATEPYIVGHNLLLAHGVAVKVYREKYQATQKGEIGIALNTAWHYPYSDSYADRLAATRATAFTFDYFMEPIVYGRYPIEMVSHVKDGRLPTFTPEESEMLKGSYDFIGVNYYSSLYAKDVPCATENITMTTDSCVSLVGERNGVPIGPAAGSDWLLIYPKGIRDLLLHAKFRYNDPVLYITENGVDEANIGKIFLNDDLRIDYYAHHLKMVSDAISIGVNVKGYFAWSLMDNFEWSEGYTVRFGLVFVDFEDGRKRYLKKSAKWFRRLLKGAHGGTNEQVAVI* Microarray datashows that the coding sequence was expressed in the followingexperiments, which shows that the promoter would be useful to modulateexpression in situations similar to the following: CDNA_ID SHORT_NAMEEXPT_REP_ID IS_UP 12668112 At_4deg_Cold 20000214 − 12668112At_10percent_PEG 20000527 − 12668112 At_Drought_Soil_Dry 20001554 −12668112 At_Drought_Soil_Dry 20001555 − 12668112 At_Interploidy_Crosses20001853 − 12668112 At_8deg_Cold 20002105 − The parameters for themicroarray experiments listed above by Expt_Rep_ID and Short_Name are asfollow below: CDNA_ID SHORT_NAME EXPT_REP_ID PARAM_NAME VALUE 12668112At_4deg_Cold 20000214 Timepoint (hr) 6 12668112 At_10percent_PEG20000527 Age (day) 20 12668112 At_10percent_PEG 20000527 Timepoint (day)20 12668112 At_10percent_PEG 20000527 Treatment 10 percent PEG vs. NoTreatment 12668112 At_10percent_PEG 20000527 Organism A. thaliana12668112 At_10percent_PEG 20000527 Tissue Whole Plant 12668112At_10percent_PEG 20000527 Plant Line WS 12668112 At_Drought_Soil_Dry20001554 Timepoint (day) 7 12668112 At_Drought_Soil_Dry 20001554 Age(day) 21 12668112 At_Drought_Soil_Dry 20001554 Organism A. thaliana12668112 At_Drought_Soil_Dry 20001554 Treatment Drought vs. No Drought12668112 At_Drought_Soil_Dry 20001554 Post Timepoint (hr) None 12668112At_Drought_Soil_Dry 20001554 Post-Treatment None 12668112At_Drought_Soil_Dry 20001554 Plant Line WS 12668112 At_Drought_Soil_Dry20001555 Timepoint (day) 10 12668112 At_Drought_Soil_Dry 20001555 Age(day) 24 12668112 At_Drought_Soil_Dry 20001555 Organism A. thaliana12668112 At_Drought_Soil_Dry 20001555 Treatment Drought vs. No Drought12668112 At_Drought_Soil_Dry 20001555 Post Timepoint (hr) None 12668112At_Drought_Soil_Dry 20001555 Post-Treatment None 12668112At_Drought_Soil_Dry 20001555 Plant Line WS 12668112At_Interploidy_Crosses 20001853 Age (day) 5 12668112At_Interploidy_Crosses 20001853 Organism A. thaliana 12668112At_Interploidy_Crosses 20001853 Plant Line Columbia 12668112At_Interploidy_Crosses 20001853 Cross Fis1 vs. 2X × 2X 12668112At_Interploidy_Crosses 20001853 Tissue Siliques 12668112 At_8deg_Cold20002105 Age (day) 7 12668112 At_8deg_Cold 20002105 Timepoint (hr) 812668112 At_8deg_Cold 20002105 Temperature (deg C.) 8 vs. 22 12668112At_8deg_Cold 20002105 Organism A. thaliana 12668112 At_8deg_Cold20002105 Tissue Whole Plant 12668112 At_8deg_Cold 20002105 Plant Line WSPromoter YP0244 Modulates the gene: Ca2+-ATPase 7 The GenBankdescription of the gene: NM_127860 Arabidopsis thaliana potentialcalcium- transporting ATPase 7, plasma membrane-type (Ca2+-ATPase,isoform 7) (At2g22950) mRNA, complete cdsgi|18400128|ref|NM_127860.1|[18400128] The promoter sequence:5′aaagtcttatttgtgaaattttacaaatgttggaaaaaagcattttatggtgctatatttgtcaatttcccttgattatatatccttttgaaaagtaatgttttttttatgtgtgtgtattcatgaaccttggaaaaactacaaatcagatcatggtttgttttaggtgaaaaatttagaacacagttacgcaagaaagatatcggtaaatttttgtttctttgaatcgaaattaatcaaaaagtattttccattatataacaacaactaatctctgttttttttttttttttttaacaactaatctcttatcaaaatgacactacagaatcacgattgtaaatctttaaaaggcagtctgaaaaatattcatgaggatgagattttattcattcatggttgtaagtaatcattatgtaaagtttaggataaggacgttcaaaatcatataaaaaaactctacgaataaagtttatagtctatcatattgattcatatttcatagaaagttactggaaaacattacacaagtattctcgatttttacgagtttgtttagtagtcgcaaaattttattttacttttgagtatacgaacccataagctgattttctttccaagttccaataatgatatcatagtgtactcttcatgaatgtttcaagcatataattataacgttcataagtaatattctactgcatgtttgttatTATAaattaactaataatcgaacgtatgagttttgattgagattgttgtgctcacgaaatgaaggactcggtcaattctaaagcttaaaataagaagctcagatcttaaaactcgctttcgtcttcgtcctccatttaagtttgcgattcttttgctcttctttctctctcacatttttgtcccaaaacaataaaaagaaacaataatagaaagtgttacagaaaaagaaagaaaac 3′-ATG The promoter was cloned from theorganism: Arabidopsis thaliana, WS ecotype Alternative nucleotides:Predicted (Columbia) Experimental (Wassilewskija) Sequence Position (bp)Mismatch Columbia/Wassilewskija 90 SNP a/g 183 SNP t/c 373 SNP t/c 380No g in Ws —/— 393 No a in Ws —/— 717 SNP t/c 774 SNP a/g The promoterwas cloned in the vector: pNewbin4-HAP1-GFP When cloned into the vectorthe promoter was operably linked to a marker, which was the type: GFP-ERPromoter-marker vector was tested in: Arabidopsis thaliana, WS ecotypeGeneration screened: XT1 Mature   XT2 Seedling   T2 Mature   T3 SeedlingThe spatial expression of the promoter-marker vector was found observedin and would be useful in expression in any or all of the following:Flower H pollen Observed expression pattern of the promoter-markervector was in: T1 mature: Pollen specific expression in mature plants.T2 seedling: No GFP expression observed. The promoter can be of use inthe following trait and sub-trait areas: (search for the trait andsub-trait table) Trait Area: Paternal inheritance trait where 50% isdesired Sub-trait Area: Yield The promoter has utility in: Utility:Modulation of pollen tube growth, incompatibility. Misc. promoterinformation: Bidirectionality: Pass Exons: Pass Repeats: No The CerescDNA ID of the endogenous coding sequence to the promoter: 12736016 cDNAnucleotide sequence:atggagagttacctcaactcgaatttcgacgttaaggcgaagcattcgtcggaggaagtgctagaaaaatggcggaatctttgcagtgtcgtcaagaacccgaaacgtcggtttcgattcactgccaatctctccaaacgttacgaagctgctgccatgcgccgcaccaaccaggagaaattaaggattgcagttctcgtgtcaaaagccgcatttcaatttatctctggtgtttctccaagtgactacaaggtgcctgaggaagttaaagcagcaggctttgacatttgtgcagacgagttaggatcaatagtggaaggtcatgatgtgaagaagctcaagttccatggtggtgttgatggtctttcaggtaagctcaaggcatgtcccaatgctggtctctcaacaggtgaacctgagcagttaagcaaacgacaagagcttttcggaatcaataagtttgcagagagtgaattacgaagtttctgggtgtttgtttgggaagcacttcaagatatgactcttatgattcttggtgtttgtgctttcgtctctttgattgttgggattgcaactgaaggatggcctcaaggatcgcatgatggtcttggcattgttgctagtattcttttagttgtgtttgtgacagcaactagtgactatagacaatctttgcagttccgggatttggataaagagaagaagaagatcacggttcaagttacgcgaaacgggtttagacaaaagatgtctatatatgatttgctccctggagatgttgttcatcttgctatcggagatcaagtccctgcagatggtcttttcctctcgggattctctgttgttatcgatgaatcgagtttaactggagagagtgagcctgtgatggtgactgcacagaaccctttccttctctctggaaccaaagttcaagatgggtcatgtaagatgttggttacaacagttgggatgagaactcaatggggaaagttaatggcaacacttagtgaaggaggagatgacgaaactccgttgcaggtgaaacttaatggagttgcaaccatcattgggaaaattggtctttccttcgctattgttacctttgcggttttggtacaaggaatgtttatgaggaagctttcattaggccctcattggtggtggtccggagatgatgcattagagcttttggagtattttgctattgctgtcacaattgttgttgttgcggttcctgaaggtttaccattagctgtcacacttagtctcgcgtttgcgatgaagaagatgatgaacgataaagcgcttgttcgccatttagcagcttgtgagacaatgggatctgcaactaccatttgtagtgacaagactggtacattaacaacaaatcacatgactgttgtgaaatcttgcatttgtatgaatgttcaagatgtagctagcaaaagttctagtttacaatctgatatccctgaagctgccttgaaactacttctccagttgatttttaataataccggtggagaagttgttgtgaacgaacgtggcaagactgagatattggggacaccaacagagactgctatattggagttaggactatctcttggaggtaagtttcaagaagagagacaatctaacaaagttattaaagttgagccttttaactcaacaaagaaaagaatgggagtagtcattgagctgcctgaaggaggacgcattcgcgctcacacgaaaggagcttcagagatagttttagcggcttgtgataaagtcatcaactcaagtggtgaagttgttccgcttgatgatgaatccatcaagttcttgaatgttacaatcgatgagtttgcaaatgaagctcttcgtactctttgccttgcttatatggatatcgaaagcgggttttcggctgatgaaggtattccggaaaaagggtttacatgcatagggattgttggtatcaaagaccctgttcgtcctggagttcgggagtccgtggaactttgtcgccgtgcgggtattatggtgagaatggttacaggagataacattaacaccgcaaaggctattgctagagaatgtggaattctcactgatgatggtatagcaattgaaggtcctgtgtttagagagaagaaccaagaagagatgcttgaactcattcccaagattcaggtcatggctcgttcttccccaatggacaagcatacactggtgaagcagttgaggactacttttgatgaagttgttgctgtgactggcgacgggacaaacgatgcaccagcgctccacgaggctgacataggattagcaatgggcattgccgggactgaagtagctaaagagattgcggatgtcatcattctcgacgataacttcagcacaatcgtcaccgtagcgaaatggggacgttctgtttacattaacattcagaaatttgtgcagtttcaactaacagtcaatgttgttgcccttattgttaacttctcttcagcttgcttgactggaagtgctcctctaactgctgttcaactgctttgggttaacatgatcatggacacacttggagctcttgctctagctacagaacctccgaacaacgagctgatgaaacgtatgcctgttggaagaagagggaatttcattaccaatgcgatgtggagaaacatcttaggacaagctgtgtatcaatttattatcatatggattctacaggccaaagggaagtccatgtttggtcttgttggttctgactctactctcgtattgaacacacttatcttcaactgctttgtattctgccaggttttcaatgaagtaagctcgcgggagatggaagagatcgatgttttcaaaggcatactcgacaactatgttttcgtggttgttattggtgcaacagttttctttcagatcataatcattgagttcttgggcacatttgcaagcaccacacctcttacaatagttcaatggttcttcagcattttcgttggcttcttgggtatgccgatcgctgctggcttgaagaaaatacccgtgtgaCoding sequence:MESYLNSNFDVKAKHSSEEVLEKWRNLCSVVKNPKRRFRFTANLSKRYEAAAMRRTNQEKLRTAVLVSKAAFQFISGVSPSDYKVPEEVKAAGFDICADELGSIVEGHDVKKLKFHGGVDGLSGKLKACPNAGLSTGEPEQLSKRQELFGINKFAESELRSFWVFVWEALQDMTLMILGVCAFVSLIVGIATEGWPQGSHDGLGIVASILLVVFVTATSDYRQSLQFRDLDKEKKKITVQVTRNGFRQKMSIYDLLPGDVVHLAIGDQVPADGLFLSGFSVVIDESSLTGESEPVMVTAQNPFLLSGTKVQDGSCKMLVTTVGMRTQWGKLMATLSEGGDDETPLQVKLNGVATIIGKIGLSFAIVTFAVLVQGMFMRKLSLGPHWWWSGDDALELLEYFAIAVTIVVVAVPEGLPLAVTLSLAFAMKKMMNDKALVRHLAACETMGSATTICSDKTGTLTTNHMTVVKSCICMNVQDVASKSSSLQSDIPEAALKLLLQLIFNNTGGEVVVNERGKTEILGTPTETAILELGLSLGGKFQEERQSNKVIKVEPFNSTKKRMGVVIELPEGGRIRAHTKGASEIVLAACDKVINSSGEVVPLDDESIKFLNVTIDEFANEALRTLCLAYMDIESGFSADEGIPEKGFTCIGIVGIKDPVRPGVRESVELCRRAGIMVRMVTGDNINTAKAIARECGILTDDGIAIEGPVFREKNQEEMLELIPKIQVMARSSPMDKHTLVKQLRTTFDEVVAVTGDGTNDAPALHEADIGLAMGIAGTEVAKEIADVIILDDNFSTIVTVAKWGRSVYINIQKFVQFQLTVNVVALIVNFSSACLTGSAPLTAVQLLWVNMIMDTLGALALATEPPNNELMKRMPVGRRGNFITNAMWRNILGQAVYQFIIIWILQAKGKSMFGLVGSDSTLVLNTLIFNCFVFCQVFNEVSSREMEEIDVFKGILDNYVFVVVIGATVFFQIIIIEFLGTFASTTPLTIVQWFFSIFVGFLGMPIAAGLKKIPV* Microarray data shows that the coding sequencewas expressed in the following experiments, which shows that thepromoter would be useful to modulate expression in situations similar tothe following: Promoter YP0226 Modulates the gene: Indoleaceticacid-induced protein 12 The GenBank description of the gene: NM_100334Arabidopsis thaliana auxin-responsive protein IAA12 (Indoleaceticacid-induced protein 12) (At1g04550) mRNA, complete cdsgi|30678909|ref|NM_100334.2 The promoter sequence:5′tcaaaagtgtaatttccacaaaccaattgcgcctgcaaaagttttcaaaggatcatcaaacataatgatgaatatctcatcaccacgattttataataatgcatcttttcccaccattttttttccctcactttcttttataatcttgttcgacaacaatcatggtctaaggaaaaagttgaaaatatatattatcttagttattagaaaagaaagataatcaaatggtcaatatgcaaatggcatatgaccataaacgagtttgctagtataaagaatgatggccaacctgttaaagagagactaaaattaggtctaaaatctaggagcaatgtaaccaatacatagtatatgaaatataaaagttaatttagattttttgattagcccaaattaaagaaaaatggtatttaaaacagagactcttcatcctaaaggctaaagcaatacaatttttggttaagaaaagaaaaaaaccacaagcggaaaagaaaacaaaaaagaactatattatgatgcaacagcaacacaaagcaaaaccttgcacacacacatacaactgtaaacaagtttcttgggactctctattttctcttgctgcttgaaccaaacacaacaacgatatcccaacgagagcacaacaggtttgattatgtcggaagacaagttttgagagaaaacaaacaatatttTATAacaaaggagaagacttttggttagaaaaaattggtatggccattacaagacatatgggtcccaattctcatcactctctccaccaccaaaatcctcctctctctctctctcttttactctgttttcatcatctctttctctcgtctctctcaaaccctaaatacactctttctcttcttgttgtctccattctctctgtgtcatcaagcttcttttttgtgtgggttatttgaaagacactttctctgctggtatcattggagt 3′-ATG The promoter was clonedfrom the organism:   Arabidopsis thaliana, WS ecotype Alternativenucleotides: Sequence (bp) Mismatch Columbia/Wassilewskija 523 SNP g/—558 SNP a/c 741 SNP a/g The promoter was cloned in the vector:pNewbin4-HAP1-GFP When cloned into the vector the promoter was operablylinked to a marker, which was the type: GFP-ER Promoter-marker vectorwas tested in:  Arabidopsis thaliana, WS ecotype Generation screened:XT1 Mature   XT2 Seedling   T2 Mature   T3 Seedling The spatialexpression of the promoter-marker vector was found observed in and wouldbe useful in expression in any or all of the following: Flower Mvascular Silique M placenta, M vascular Hypocotyl H vascular Cotyledon Hvascular, H petiole Primary Root H vascular Observed expression patternof the promoter-marker vector was in: T1 mature: GFP expressed invasculature of silique and pedicles of flowers. T2 seedling: High GFPexpression throughout vasculature of root, hypocotyl, and petioles.Misc. promoter information:   Bidirectionality: Pass   Exons: Pass   Repeats: No Optional Promoter Fragments: 5′ UTR region at base pairs832-1000 The Ceres cDNA ID of the endogenous coding sequence to thepromoter: 12327003 cDNA nucleotide sequence:ACTCTGTTTTCATCATCTCTTTCTCTCGTCTCTCTCAAACCCTAAATACACTCTTTCTCTTCTTGTTGTCTCCATTCTCTCTGTGTCATCAAGCTTCTTTTTTGTGTGGGTTATTTGAAAGACACTTTCTCTGCTGGTATCATTGGAGTCTAGGGTTTTGTTATTGACATGCGTGGTGTGTCAGAATTGGAGGTGGGGAAGAGTAATCTTCCGGCGGAGAGTGAGCTGGAATTGGGATTAGGGCTCAGCCTCGGTGGTGGCGCGTGGAAAGAGCGTGGGAGGATTCTTACTGCTAAGGATTTTCCTTCCGTTGGGTCTAAACGCTCTGCTGAATCTTCCTCTCACCAAGGAGCTTCTCCTCCTCGTTCAAGTCAAGTGGTAGGATGGCCACCAATTGGGTTACACAGGATGAACAGTTTGGTTAATAACCAAGCTATGAAGGCAGCAAGAGCGGAAGAAGGAGACGGGGAGAAGAAAGTTGTGAAGAATGATGAGCTCAAAGATGTGTCAATGAAGGTGAATCCGAAAGTTCAGGGCTTAGGGTTTGTTAAGGTGAATATGGATGGAGTTGGTATAGGCAGAAAAGTGGATATGAGAGCTCATTCGTCTTACGAAAACTTGGCTCAGACGCTTGAGGAAATGTTCTTTGGAATGACAGGTACTACTTGTCGAGAAAAGGTTAAACCTTTAAGGCTTTTAGATGGATCATCAGACTTTGTACTCACTTATGAAGATAAGGAAGGGGATTGGATGCTTGTTGGAGATGTTCCATGGAGAATGTTTATCAACTCGGTGAAAAGGCTTCGGATCATGGGAACCTCAGAAGCTAGTGGACTAGCTCCAAGACGTCAAGAGCAGAAGGATAGACAAAGAAACAACCCTGTTTAGCTTCCCTTCCAAAGCTGGCATTGTTTATGTATTGTTTGAGGTTTGCAATTTACTCGATACTTTTTGAAGAAAGTATTTTGGAGAATATGGATAAAAGCATGCAGAAGCTTAGATATGATTTGAATCCGGTTTTCGGATATGGTTTTGCTTAGGTCATTCAATTCGTAGTTTTCCAGTTTGTTTCTTCTTTGGCTGTGTACCAATTATCTATGTTCTGTGAGAGAAAGCTCTTGTTTATTTGTTCTCTCAGATTGTAAATAGTTGAAGTTATCTAATTAATGTGATAAGAGTTATGTTTATGATTCC Coding sequence:MRGVSELEVGKSNLPAESELELGLGLSLGGGAWKERGRILTAKDFPSVGSKRSAESSSHQGASPPRSSQVVGWPPIGLHRMNSLVNNQAMKAARAEEGDGEKKVVKNDELKDVSMKVNPKVQGLGFVKVNMDGVGIGRKVDMRAHSSYENLAQTLEEMFFGMTGTTCREKVKPLRLLDGSSDFVLTYEDKEGDWMLVGDVPWRMFINSVKRLRIMGTSEASGLAPRRQEQKDRQRNNPV* Microarray data showsthat the coding sequence was expressed in the following experiments,which shows that the promoter would be useful to modulate expression insituations similar to the following: CDNA_ID SHORT_NAME EXPT_REP_IDIS_UP 12327003 At_Diversity_Expt 108457 − 12327003 At_100uM_ABA 108561 −12327003 At_100uM_ABA_Mutants 20000069 − 12327003 At_100uM_ABA_Mutants20000070 − 12327003 At_100uM_ABA_Mutants 20000072 − 12327003At_100uM_ABA_Mutants 20000086 − 12327003 At_100uM_ABA_Mutants 20000087 −12327003 At_100uM_ABA_Mutants 20000088 − 12327003At_2mM_SA_CS3726-Columbia 20000089 − 12327003 At_100uM_ABA_Mutants20000117 − 12327003 At_Far-red-induction 20001248 − 12327003At_8deg_Cold 20002105 + The parameters for the microarray experimentslisted above by Expt_Rep_ID and Short_Name are as follow below: CDNA_IDSHORT_NAME EXPT_REP_ID PARAM_NAME VALUE 12327003 At_Diversity_Expt108457 Plant Line Canola vs. WS 12327003 At_Diversity_Expt 108457 TissueHypocotyl 12327003 At_100uM_ABA 108561 Timepoint (hr) 6 12327003At_100uM_ABA 108561 Treatment 100 uM ABA vs. No Treatment 12327003At_100uM_ABA 108561 Tissue Aerial 12327003 At_100uM_ABA_Mutants 20000069Timepoint (hr) 6 12327003 At_100uM_ABA_Mutants 20000069 Treatment 100 uMABA vs. No Treatment 12327003 At_100uM_ABA_Mutants 20000069 TissueAerial 12327003 At_100uM_ABA_Mutants 20000069 Plant Line CS23 12327003At_100uM_ABA_Mutants 20000070 Timepoint (hr) 6 12327003At_100uM_ABA_Mutants 20000070 Treatment 100 uM ABA vs. No Treatment12327003 At_100uM_ABA_Mutants 20000070 Tissue Aerial 12327003At_100uM_ABA_Mutants 20000070 Plant Line CS24 12327003At_100uM_ABA_Mutants 20000072 Timepoint (hr) 6 12327003At_100uM_ABA_Mutants 20000072 Treatment 100 uM ABA vs. No Treatment12327003 At_100uM_ABA_Mutants 20000072 Tissue Aerial 12327003At_100uM_ABA_Mutants 20000072 Plant Line CS8105 12327003At_100uM_ABA_Mutants 20000086 Timepoint (hr) 6 12327003At_100uM_ABA_Mutants 20000086 Treatment 100 uM ABA vs. No Treatment12327003 At_100uM_ABA_Mutants 20000086 Tissue Aerial 12327003At_100uM_ABA_Mutants 20000086 Plant Line CS22 12327003At_100uM_ABA_Mutants 20000087 Timepoint (hr) 6 12327003At_100uM_ABA_Mutants 20000087 Treatment 100 uM ABA vs. No Treatment12327003 At_100uM_ABA_Mutants 20000087 Tissue Aerial 12327003At_100uM_ABA_Mutants 20000087 Plant Line WS 12327003At_100uM_ABA_Mutants 20000088 Timepoint (hr) 6 12327003At_100uM_ABA_Mutants 20000088 Treatment 100 uM ABA vs. No Treatment12327003 At_100 uM_ABA_Mutants 20000088 Tissue Aerial 12327003At_100uM_ABA_Mutants 20000088 Plant Line Landsberg 12327003At_2mM_SA_CS3726- 20000089 Timepoint (hr) 6 Columbia 12327003At_2mM_SA_CS3726- 20000089 Treatment 2 mM SA vs. No Treatment Columbia12327003 At_2mM_SA_CS3726- 20000089 Tissue Aerial Columbia 12327003At_2mM_SA_CS3726- 20000089 Plant Line CS3726 Columbia 12327003At_100uM_ABA_Mutants 20000117 Timepoint (hr) 6 12327003At_100uM_ABA_Mutants 20000117 Treatment 100 uM ABA vs. No Treatment12327003 At_100uM_ABA_Mutants 20000117 Tissue Aerial 12327003At_100uM_ABA_Mutants 20000117 Plant Line Columbia 12327003At_Far-red-induction 20001248 Timepoint (hr) 4 12327003At_Far-red-induction 20001248 Age (day) 7 12327003 At_Far-red-induction20001248 Organism A. thaliana 12327003 At_Far-red-induction 20001248Plant Line Columbia 12327003 At_Far-red-induction 20001248 Light Far-redvs. White 12327003 At_Far-red-induction 20001248 Tissue Whole Plant12327003 At_8deg_Cold 20002105 Age (day) 7 12327003 At_8deg_Cold20002105 Timepoint (hr) 8 12327003 At_8deg_Cold 20002105 Temperature(deg C.) 8 vs. 22 12327003 At_8deg_Cold 20002105 Organism A. thaliana12327003 At_8deg_Cold 20002105 Tissue Whole Plant 12327003 At_8deg_Cold20002105 Plant Line WS Promoter PT0511 Modulates the gene: Majorintrinsic protein (MIP) The GenBank description of the gene:: NM_106724Arabidopsis thaliana major intrinsic protein (MIP) family (At1g80760)mRNA, complete cds gi|30699534|ref|NM_106724.2|[30699534]. The promotersequence:5′gacgggtcatcacagattcttcgtttttttatagatagaaaaggaataacgttaaaagtatacaaattatatgcaagagtcattcgaaagaattaaataaagagatgaactcaaaagtgattttaaattttaatgataagaatatacatctcacagaaatcttttatttgacatgtaaaatcttgttttcacctatcttttgttagtaaacaagaatatttaatttgagcctcacttggaacgtgataataatatacatcttatcataattgcatattttgcggatagtttttgcatggggagattaaaggcttaataaagccttgaatttccgaggggaggaatcatgttttatacttgcaaactatacaaccatctgcatcgataattggtgttaatacatgcaaggattatacactaaaacaaatcatttatttccttacaaaaagagagtcgactgtgagtcacattctgtgacaaggaaaggtcaagaaccatcgcttttatcatcattctctttgctaacaacttacaaccacacaaacgcaagagttccattctcatggagaagaacatattatgcaaaataatgtatgtcgatcgatagagaaaaggatccacaattattgctccatctcaaaagcttctttagtacacgatacatgtatcatgtaaatagaaatatgaaagatacaatacacgacccattctcataaagatagcaacatttcatgttatgtaaagagtcttccttaggacacatgcattaaaactaaggattaccaacccacttactcctcactccaaccaaatatcaatcatctattttgggtccttcactcataagtcaactctcatgccttcctctataaataccgtaccctacgcatcccttagttctacatcacataaaaacaatcatagcaaaaacaTATAtcctcaaattaatt 3′-cATG The promoter was cloned from theorganism:   Arabidopsis thaliana, Columbia ecotype Alternativenucleotides: Predicted Position (bp) Mismatch Predicted/Experimental1-1000 None Identities = 1000/1000 (100%) The promoter was cloned in thevector:  pNewbin4-HAP1-GFP When cloned into the vector the promoter wasoperably linked to a marker, which was the type: GFP-ER Promoter-markervector was tested in: Arabidopsis thaliana, WS ecotype Generationscreened: XT1 Mature   XT2 Seedling   T2 Mature   T3 Seedling Thespatial expression of the promoter-marker vector was found observed inand would be useful in expression in any or all of the following: FlowerH filament H anther L vascular Cotyledon L vascular L petiole PrimaryRoot L epidermis Observed expression pattern of the promoter-markervector was in: T1 mature: High expression at vascular connective tissuebetween locules of anther. T2 seedling: Low expression in root epidermalcells and vasculature of petioles. Misc. promoter information:  Bidirectionality: Pass   Exons: Pass    Repeats: No Optional PromoterFragments: 5′ UTR region at base pairs 927-1000. The Ceres cDNA ID ofthe endogenous coding sequence to the promoter: 12711931 cDNA nucleotidesequence:ATGGATCATGAGGAAATTCCATCCACGCCCTCAACGCCGGCGACAACCCCGGGGACTCCAGGAGCGCCGCTCTTTGGAGGATTCGAAGGGAAGAGGAATGGACACAATGGTAGATACACACCAAAGTCACTTCTCAAAAGCTGCAAATGTTTCAGTGTTGACAATGAATGGGCTCTTGAAGATGGAAGACTCCCTCCGGTCACTTGCTCTCTCCCTCCCCCTAACGTTTCCCTCTACCGCAAGTTGGGAGCAGAGTTTGTTGGGACATTGATCCTGATATTCGCCGGAACAGCGACGGCGATCGTGAACCAGAAGACAGATGGAGCTGAGACGCTTATTGGTTGCGCCGCCTCGGCTGGTTTGGCGGTTATGATCGTTATATTATCGACCGGTCACATCTCCGGGGCACATCTCAATCCGGCTGTAACCATTGCCTTTGCTGCTCTCAAACACTTCCCTTGGAAACACGTGCCGGTGTATATCGGAGCTCAGGTGATGGCCTCCGTGAGTGCGGCGTTTGCACTGAAAGCAGTGTTTGAACCAACGATGAGCGGTGGCGTGACGGTGCCGACGGTGGGTCTCAGCCAAGCTTTCGCCTTGGAATTCATTATCAGCTTCAACCTCATGTTCGTTGTCACAGCCGTAGCCACCGACACGAGAGCTGTGGGAGAGTTGGCGGGAATTGCCGTAGGAGCAACGGTCATGCTTAACATACTTATAGCTGGACCTGCAACTTCTGCTTCGATGAACCCTGTAAGAACACTGGGTCCAGCCATTGCAGCAAACAATTACAGAGCTATTTGGGTTTACCTCACTGCCCCCATTCTTGGAGCGTTAATCGGAGCAGGTACATACACAATTGTCAAGTTGCCAGAGGAAGATGAAGCACCCAAAGAGAGGAGGAGCTTCAGAAGATGA Coding sequence:MDHEEIPSTPSTPATTPGTPGAPLFGGFEGKRNGHNGRYTPKSLLKSCKCFSVDNEWALEDGRLPPVTCSLPPPNVSLYRKLGAEFVGTLILIFAGTATAIVNQKTDGAETLIGCAASAGLAVMIVILSTGHISGAHLNPAVTIAFAALKHFPWKHVPVYIGAQVMASVSAAFALKAVFEPTMSGGVTVPTVGLSQAFALEFIISFNLMFVVTAVATDTRAVGELAGIAVGATVMLNILIAGPATSASMNPVRTLGPAIAANNYRAIWVYLTAPILGALIGAGTYTIVKLPEEDEAPKERRSFRR* Microarray data shows that thecoding sequence was expressed in the following experiments, which showsthat the promoter would be useful to modulate expression in situationssimilar to the following: CDNA_ID SHORT_NAME EXPT_REP_ID IS_UP 12711931At_Root_Tips 108434 − 12711931 At_stm_Mutants 108435 + 12711931At_Diversity_Expt 108457 + 12711931 At_Diversity_Expt 108458 + 12711931At_Germinating_Seeds 108464 + 12711931 At_ap2_floral_buds 108501 +12711931 At_4deg_Cold 108579 + 12711931 At_Ler-pi_Ovule 108595 +12711931 At_100uM_ABA_Mutants 20000069 − 12711931 At_100uM_ABA_Mutants20000070 − 12711931 At_100uM_ABA_Mutants 20000071 − 12711931At_100uM_ABA_Mutants 20000086 − 12711931 At_100uM_ABA_Mutants 20000087 −12711931 At_100uM_ABA_Mutants 20000088 − 12711931At_2mM_SA_CS3726-Columbia 20000089 − 12711931 At_2mM_SA_CS3726-Columbia20000090 − 12711931 At_100uM_ABA_Mutants 20000117 − 12711931At_CS6632_Shoots-Roots 20000224 + 12711931 At_Root-Tips-vs-Tops20000227 + 12711931 At_Siliques 20000234 + 12711931 At_Siliques20000236 + 12711931 At_Caf_Knockout 20000244 − 12711931 At_Open_Flower20000264 + 12711931 At_Open_Flower 20000286 + 12711931 At_Drought20000437 − 12711931 At_Shoots 20000438 + 12711931 At_CS6879_Shoots-Roots20000451 − 12711931 At_42deg_Heat 20000458 − 12711931 At_Guard_Cells20000495 + 12711931 At_100uM_ABA_Mutants 20000576 + 12711931At_Herbicide_Mutants 20000640 − 12711931 At_Herbicide_Mutants 20000642 −12711931 At_Petals 20000794 + 12711931 At_Line_Comparisons 20001151 +12711931 At_Line_Comparisons 20001184 + 12711931 At_Far-red-induction20001248 − 12711931 At_Line_Comparisons 20001307 + 12711931At_Line_Comparisons 20001318 + 12711931 At_Line_Comparisons 20001319 +12711931 At_Line_Comparisons 20001347 + 12711931 At_50mM_NH4NO3_L-to-H20001458 − 12711931 At_Drought_Soil_Dry 20001556 − 12711931At_Drought_Soil_Dry 20001557 − 12711931 At_Drought_Soil_Dry 20001558 −12711931 At_Drought_Reproduction 20001905 − 12711931At_Drought_Reproduction 20001906 − 12711931 At_Drought_Reproduction20001907 − 12711931 At_8deg_Cold 20002105 + The parameters for themicroarray experiments listed above by Expt_Rep_ID and Short_Name are asfollow below: CDNA_ID SHORT_NAME EXPT_REP_ID PARAM_NAME VALUE 12711931At_Root_Tips 108434 Tissue Root Tips 12711931 At_stm_Mutants 108435Tissue Shoot Apical Meristem Region 12711931 At_stm_Mutants 108435 PlantLine wt Landsburg vs stm 12711931 At_Diversity_Expt 108457 Plant LineCanola vs. WS 12711931 At_Diversity_Expt 108457 Tissue Hypocotyl12711931 At_Diversity_Expt 108458 Plant Line Holbolliie vs. WS 12711931At_Diversity_Expt 108458 Tissue Hypocotyl 12711931 At_Germinating_Seeds108464 Age (day) 4 vs. 0 12711931 At_Germinating_Seeds 108464 TissueGerminating Seeds 12711931 At_ap2_floral_buds 108501 Plant Line ap2(Ler.) 12711931 At_ap2_floral_buds 108501 Tissue Closed Flower 12711931At_4deg_Cold 108579 Timepoint (hr) 6 12711931 At_4deg_Cold 108579Temperature (deg C.) 4 vs. 22 12711931 At_4deg_Cold 108579 Tissue Aerial12711931 At_Ler-pi_Ovule 108595 Plant Line Ler_pi 12711931At_Ler-pi_Ovule 108595 Tissue Ovules 12711931 At_100uM_ABA_Mutants20000069 Timepoint (hr) 6 12711931 At_100uM_ABA_Mutants 20000069Treatment 100 uM ABA vs. No Treatment 12711931 At_100uM_ABA_Mutants20000069 Tissue Aerial 12711931 At_100uM_ABA_Mutants 20000069 Plant LineCS23 12711931 At_100uM_ABA_Mutants 20000070 Timepoint (hr) 6 12711931At_100uM_ABA_Mutants 20000070 Treatment 100 uM ABA vs. No Treatment12711931 At_100uM_ABA_Mutants 20000070 Tissue Aerial 12711931At_100uM_ABA_Mutants 20000070 Plant Line CS24 12711931At_100uM_ABA_Mutants 20000071 Timepoint (hr) 6 12711931At_100uM_ABA_Mutants 20000071 Treatment 100 uM ABA vs. No Treatment12711931 At_100uM_ABA_Mutants 20000071 Tissue Aerial 12711931At_100uM_ABA_Mutants 20000071 Plant Line CS8104 12711931At_100uM_ABA_Mutants 20000086 Timepoint (hr) 6 12711931At_100uM_ABA_Mutants 20000086 Treatment 100 uM ABA vs. No Treatment12711931 At_100uM_ABA_Mutants 20000086 Tissue Aerial 12711931At_100uM_ABA_Mutants 20000086 Plant Line CS22 12711931At_100uM_ABA_Mutants 20000087 Timepoint (hr) 6 12711931At_100uM_ABA_Mutants 20000087 Treatment 100 uM ABA vs. No Treatment12711931 At_100uM_ABA_Mutants 20000087 Tissue Aerial 12711931At_100uM_ABA_Mutants 20000087 Plant Line WS 12711931At_100uM_ABA_Mutants 20000088 Timepoint (hr) 6 12711931At_100uM_ABA_Mutants 20000088 Treatment 100 uM ABA vs. No Treatment12711931 At_100uM_ABA_Mutants 20000088 Tissue Aerial 12711931At_100uM_ABA_Mutants 20000088 Plant Line Landsberg 12711931At_2mM_SA_CS3726- 20000089 Timepoint (hr) 6 Columbia 12711931At_2mM_SA_CS3726- 20000089 Treatment 2 mM SA vs. No Treatment Columbia12711931 At_2mM_SA_CS3726- 20000089 Tissue Aerial Columbia 12711931At_2mM_SA_CS3726- 20000089 Plant Line CS3726 Columbia 12711931At_2mM_SA_CS3726- 20000090 Timepoint (hr) 6 Columbia 12711931At_2mM_SA_CS3726- 20000090 Treatment 2 mM SA vs. No Treatment Columbia12711931 At_2mM_SA_CS3726- 20000090 Tissue Aerial Columbia 12711931At_2mM_SA_CS3726- 20000090 Plant Line Columbia Columbia 12711931At_100uM_ABA_Mutants 20000117 Timepoint (hr) 6 12711931At_100uM_ABA_Mutants 20000117 Treatment 100 uM ABA vs. No Treatment12711931 At_100uM_ABA_Mutants 20000117 Tissue Aerial 12711931At_100uM_ABA_Mutants 20000117 Plant Line Columbia 12711931At_CS6632_Shoots-Roots 20000224 Age (day) 14 12711931At_CS6632_Shoots-Roots 20000224 Organism A. thaliana 12711931At_CS6632_Shoots-Roots 20000224 Plant Line CS6632 vs. WS 12711931At_CS6632_Shoots-Roots 20000224 Tissue Shoots 12711931At_Root-Tips-vs-Tops 20000227 Age (day) 7, 10, 14 12711931At_Root-Tips-vs-Tops 20000227 Organism A. thaliana 12711931At_Root-Tips-vs-Tops 20000227 Tissue Root Tips vs. Root Tops 12711931At_Root-Tips-vs-Tops 20000227 Plant Line WS 12711931 At_Siliques20000234 Age (day) 21 12711931 At_Siliques 20000234 Tissue <5 mmSiliques vs. Whole Plant 12711931 At_Siliques 20000234 Organism A.thaliana 12711931 At_Siliques 20000234 Plant Line WS 12711931At_Siliques 20000236 Age (day) 21 12711931 At_Siliques 20000236Tissue >10 mm Siliques vs. Whole Plant 12711931 At_Siliques 20000236Organism A. thaliana 12711931 At_Siliques 20000236 Plant Line WS12711931 At_Caf_Knockout 20000244 Plant Line caf Knockout vs. wt12711931 At_Caf_Knockout 20000244 Tissue Rosette 12711931 At_Open_Flower20000264 Age (day) 21 12711931 At_Open_Flower 20000264 Organism A.thaliana 12711931 At_Open_Flower 20000264 Tissue Open Flower vs. WholePlant 12711931 At_Open_Flower 20000264 Plant Line WS 12711931At_Open_Flower 20000286 Age (day) 21 12711931 At_Open_Flower 20000286Organism A. thaliana 12711931 At_Open_Flower 20000286 Tissue Half Openvs. Whole Plant 12711931 At_Open_Flower 20000286 Plant Line WS 12711931At_Drought 20000437 Age (day) 8 12711931 At_Drought 20000437 Timepoint(hr) 24 12711931 At_Drought 20000437 Organism A. thaliana 12711931At_Drought 20000437 Treatment Drought vs. No Drought 12711931 At_Drought20000437 Tissue Whole Plant 12711931 At_Drought 20000437 Plant Line WS12711931 At_Shoots 20000438 Age (day) 14 vs. 21 12711931 At_Shoots20000438 Organism A. thaliana 12711931 At_Shoots 20000438 Tissue Shootsvs. Whole Plant 12711931 At_Shoots 20000438 Plant Line WS 12711931At_CS6879_Shoots-Roots 20000451 Age (day) 14 12711931At_CS6879_Shoots-Roots 20000451 Organism A. thaliana 12711931At_CS6879_Shoots-Roots 20000451 Plant Line CS6879 vs. WS 12711931At_CS6879_Shoots-Roots 20000451 Tissue Roots 12711931 At_42deg_Heat20000458 Timepoint (hr) 8 12711931 At_42deg_Heat 20000458 Age (day) 1412711931 At_42deg_Heat 20000458 Temperature (deg C.) 42 vs. 22 12711931At_42deg_Heat 20000458 Organism A. thaliana 12711931 At_42deg_Heat20000458 Tissue Aerial 12711931 At_42deg_Heat 20000458 Plant Line WS12711931 At_Guard_Cells 20000495 Harvest Date 08 Feb. 2002 12711931At_Guard_Cells 20000495 Organism A. thaliana 12711931 At_Guard_Cells20000495 Tissue Guard Cells vs. Leaves 12711931 At_100uM_ABA_Mutants20000576 Timepoint (hr) 6 12711931 At_100uM_ABA_Mutants 20000576Treatment 1 uM ABA vs. No Treatment 12711931 At_100uM_ABA_Mutants20000576 Organism A. thaliana 12711931 At_100uM_ABA_Mutants 20000576Plant Line CS23 12711931 At_100uM_ABA_Mutants 20000576 Tissue WholePlant 12711931 At_Herbicide_Mutants 20000640 Timepoint (hr) 12 12711931At_Herbicide_Mutants 20000640 Plant Line 05377RR/BR27173 12711931At_Herbicide_Mutants 20000640 Treatment Roundup vs. No Treatment12711931 At_Herbicide_Mutants 20000640 Tissue Seedlings 12711931At_Herbicide_Mutants 20000642 Timepoint (hr) 12 12711931At_Herbicide_Mutants 20000642 Plant Line 3950BR/PCJE10000 12711931At_Herbicide_Mutants 20000642 Treatment Finale vs. No Treatment 12711931At_Herbicide_Mutants 20000642 Tissue Seedlings 12711931 At_Petals20000794 Age (day) 23-25 days 12711931 At_Petals 20000794 Organism A.thaliana 12711931 At_Petals 20000794 Tissue Petals vs. Whole plant12711931 At_Petals 20000794 Plant Line WS 12711931 At_Line_Comparisons20001151 Plant Line ME01339-01 vs. WS 12711931 At_Line_Comparisons20001184 Plant Line ME01848-01 vs. WS 12711931 At_Far-red-induction20001248 Timepoint (hr) 4 12711931 At_Far-red-induction 20001248 Age(day) 7 12711931 At_Far-red-induction 20001248 Organism A. thaliana12711931 At_Far-red-induction 20001248 Plant Line Columbia 12711931At_Far-red-induction 20001248 Light Far-red vs. White 12711931At_Far-red-induction 20001248 Tissue Whole Plant 12711931At_Line_Comparisons 20001307 Plant Line WBin4-WX2-A vs. WS 12711931At_Line_Comparisons 20001318 Plant Line WBin4-WX14R-A vs. WS 12711931At_Line_Comparisons 20001319 Plant Line WBin4-WX24-A vs. WS 12711931At_Line_Comparisons 20001347 Plant Line ME01604-01 vs. WS 12711931At_50mM_NH4NO3_L-to-H 20001458 Timepoint (hr) 2 12711931At_50mM_NH4NO3_L-to-H 20001458 Treatment 50 mM NH4NO3 vs. 100 mM Manitol12711931 At_50mM_NH4NO3_L-to-H 20001458 Organism A. thaliana 12711931At_50mM_NH4NO3_L-to-H 20001458 Tissue Siliques 12711931At_50mM_NH4NO3_L-to-H 20001458 Age (day) Undefined 12711931At_50mM_NH4NO3_L-to-H 20001458 Plant Line WS 12711931At_Drought_Soil_Dry 20001556 Timepoint (day) 12 12711931At_Drought_Soil_Dry 20001556 Age (day) 26 12711931 At_Drought_Soil_Dry20001556 Organism A. thaliana 12711931 At_Drought_Soil_Dry 20001556Treatment Drought vs. No Drought 12711931 At_Drought_Soil_Dry 20001556Post Timepoint (hr) None 12711931 At_Drought_Soil_Dry 20001556Post-Treatment None 12711931 At_Drought_Soil_Dry 20001556 Plant Line WS12711931 At_Drought_Soil_Dry 20001557 Post Timepoint (hr) 3 12711931At_Drought_Soil_Dry 20001557 Timepoint (day) 13 12711931At_Drought_Soil_Dry 20001557 Age (day) 27 12711931 At_Drought_Soil_Dry20001557 Organism A. thaliana 12711931 At_Drought_Soil_Dry 20001557Treatment Drought vs. No Drought 12711931 At_Drought_Soil_Dry 20001557Post-Treatment Re-Water vs. No Drought 12711931 At_Drought_Soil_Dry20001557 Plant Line WS 12711931 At_Drought_Soil_Dry 20001558 PostTimepoint (hr) 6 12711931 At_Drought_Soil_Dry 20001558 Timepoint (day)13 12711931 At_Drought_Soil_Dry 20001558 Age (day) 27 12711931At_Drought_Soil_Dry 20001558 Organism A. thaliana 12711931At_Drought_Soil_Dry 20001558 Treatment Drought vs. No Drought 12711931At_Drought_Soil_Dry 20001558 Post-Treatment Re-Water vs. No Drought12711931 At_Drought_Soil_Dry 20001558 Plant Line WS 12711931At_Drought_Reproduction 20001905 Timepoint (day) 10 12711931At_Drought_Reproduction 20001905 Age (day) 40 12711931At_Drought_Reproduction 20001905 Organism A. thaliana 12711931At_Drought_Reproduction 20001905 Treatment Drought vs. No Drought12711931 At_Drought_Reproduction 20001905 Tissue Rosettes 12711931At_Drought_Reproduction 20001905 Plant Line WS 12711931At_Drought_Reproduction 20001906 Timepoint (day) 5 12711931At_Drought_Reproduction 20001906 Age (day) 35 12711931At_Drought_Reproduction 20001906 Organism A. thaliana 12711931At_Drought_Reproduction 20001906 Treatment Drought vs. No Drought12711931 At_Drought_Reproduction 20001906 Tissue Siliques 12711931At_Drought_Reproduction 20001906 Plant Line WS 12711931At_Drought_Reproduction 20001907 Timepoint (day) 7 12711931At_Drought_Reproduction 20001907 Age (day) 37 12711931At_Drought_Reproduction 20001907 Organism A. thaliana 12711931At_Drought_Reproduction 20001907 Treatment Drought vs. No Drought12711931 At_Drought_Reproduction 20001907 Tissue Siliques 12711931At_Drought_Reproduction 20001907 Plant Line WS 12711931 At_8deg_Cold20002105 Age (day) 7 12711931 At_8deg_Cold 20002105 Timepoint (hr) 812711931 At_8deg_Cold 20002105 Temperature (deg C.) 8 vs. 22 12711931At_8deg_Cold 20002105 Organism A. thaliana 12711931 At_8deg_Cold20002105 Tissue Whole Plant 12711931 At_8deg_Cold 20002105 Plant Line WSPromoter PT0506 Modulates the gene: CYCD1 The GenBank description of thegene: NM_105689 Arabidopsis thaliana cyclin delta-1 (CYCD1) (At1g70210)mRNA, complete cds gi|30698007|ref|NM_105689.2|[30698007]. Go function:cyclin- dependent protein kinase regulator. The promoter sequence:5′cgctccagaccactgtttgctttcctctgattaaccaatctcaattaaactactaatttataattcaagataattagataaccaatcttaaaatttggaatcttcttccctcacttgatattacaaaaaaaaaactgatttatcatacggttaattcaagaaaacagcaaaaaaattgcactataatgcaaaacatcaattaattacattcgattaaaaaatcatcattgaatctaaaatggcctcaaatctattgagcatttgtcatgtgcctaaaatggttcaggagttttacatctaatcacataaaaagcaaacaataaccaaaaaaattgcattttagcaaatcaaatacttatatatatacgtatgattaagcgtcatgactttaaaacctctgtaaaattttgatttatttttcgatgcttttattttttaaccaatagtaataaagtccaaatcttaaatacgaaaaaatgtttctttctaagcgaccaacaaaatggtccaaatcacagaaaatgttccataatccaggcccattaagctaatcaccaagtaatacattacacgtcaccaattaatacattacacgtacggccttctctcttcacgagtaatatgcaaacaaacgtacattagctgtaatgtactcactcatgcaacgtcttaacctgccacgtattacgtaattacaccactccttgttcctaacctacgcatttcactttagcgcatgttagtcaaaaaacacaaacataaactacaaataaaaaaactcaaaacaaaacccaatgaacgaacggaccagccccgtctcgattgatggaacagtgacaacagtcccgttttctcgggcataacggaaacggtaaccgtctctctgtttcatttgcaacaacaccattttTATAaataaaaacacatttaaataaaaaattattaaaacc 3′-tatatccaaacaaatgaatgtgttaaaccttcactcttctctccacacaaaattcaaaaacctcacatttcacttctctcttctcgcttcttctagatctcaccggtttatctagctccggtttgattcatctccggttatggggagagaATG The promoter was cloned from the organism: Arabidopsisthaliana, Columbia ecotype Alternative nucleotides: Predicted Position(bp) Mismatch Predicted/Experimental 1-1000 None Identities = 1000/1000(100%) The promoter was cloned in the vector: pNewbin4-HAP1-GFP Whencloned into the vector the promoter was operably linked to a marker,which was the type: GFP-ER Promoter-marker vector was tested in:Arabidopsis thaliana, WS ecotype Generation screened: XT1 Mature   XT2Seedling   T2 Mature   T3 Seedling The spatial expression of thepromoter-marker vector was found observed in and would be useful inexpression in any or all of the following: Flower L anther Observedexpression pattern of the promoter-marker vector was in: T1 mature: Lowexpression in anther walls early in stamen development throughpre-dehiscence stage. Not in pollen T2 seedling: No expression observed.Misc. promoter information:  Bidirectionality: Pass   Exons: Pass   Repeats: No The Ceres cDNA ID of the endogenous coding sequence tothe promoter: 13497447 cDNA nucleotide sequence:ATATATCCAAACAAATGAATGTGTTAAACCTTCACTCTTCTCTCCACACAAAATTCAAAAACCTCACATTTCACTTCTCTCTTCTCGCTTCTTCTAGATCTCACCGGTTTATCTAGCTCCGGTTTGATTCATCTCCGGTTATGGGGAGAGAATGAGGAGTTACCGTTTTAGTGATTATCTACACATGTCTGTTTCATTCTCTAACGATATGGATTTGTTTTGTGGAGAAGACTCCGGTGTGTTTTCCGGTGAGTCAACGGTTGATTTCTCGTCTTCCGAGGTTGATTCATGGCCTGGTGATTCTATCGCTTGTTTTATCGAAGACGAGCGTCACTTCGTTCCTGGACATGATTATCTCTCTAGATTTCAAACTCGATCTCTCGATGCTTCCGCTAGAGAAGATTCCGTCGCATGGATTCTCAAGGTACAAGCGTATTATAACTTTCAGCCTTTAACGGCGTACCTCGCCGTTAACTATATGGATCGGTTTCTTTACGCTCGTCGATTACCGGAAACGAGTGGTTGGCCAATGCAACTTTTAGCAGTGGCATGCTTGTCTTTAGCTGCAAAGATGGAGGAAATTCTCGTTCCTTCTCTTTTTGATTTTCAGGTTGCAGGAGTGAAGTATTTATTTGAAGCAAAAACTATAAAAAGAATGGAACTTCTTGTTCTAAGTGTGTTAGATTGGAGACTAAGATCGGTTACACCGTTTGATTTCATTAGCTTCTTTGCTTACAAGATCGATCCTTCGGGTACCTTTCTCGGGTTCTTTATCTCCCATGCTACAGAGATTATACTCTCCAACATAAAAGAAGCGAGCTTTCTTGAGTACTGGCCATCGAGTATAGCTGCAGCCGCGATTCTCTGTGTAGCGAACGAGTTACCTTCTCTATCCTCTGTTGTCAATCCCCACGAGAGCCCTGAGACTTGGTGTGACGGATTGAGCAAAGAGAAGATAGTGAGATGCTATAGACTGATGAAAGCGATGGCCATCGAGAATAACCGGTTAAATACACCAAAAGTGATAGCAAAGCTTCGAGTGAGTGTAAGGGCATCATCGACGTTAACAAGGCCAAGTGATGAATCCTCTTTCTCATCCTCTTCTCCTTGTAAAAGGAGAAAATTAAGTGGCTATTCATGGGTAGGTGATGAAACATCTACCTCTAATTAAAATTTGGGGAGTGAAAGTAGAGGACCAAGGAAACAAAACCTAGAAGAAAAAAAACCCTCTTCTGTTTAAGTAGAGTATATTTTTTAACAAGTACATAGTAATAAGGGAGTGATGAAGAAAAGTAAAAGTGTTTATTGGCTGAGTTAAAGTAATTAAGAGTTTTCCAACCAAGGGGAAGGAATAAGAGTTTTGGTTACAATTTCTTTTATGGAAAGGGTAAAAATTGGGTTTTGGGGTTGGTTGGTTGGTTGGGAGAGACGAAGCTCATCATTAATGGCTTTGCAGATTCCCAAGAAAGCAAAATGAGTAAGTGAGTGTAACACACACGTGTTAGAGAAAAGATATGATCATGTGAGTGTGTGTGTGTGAGAGAGAGAGAGAAGAGTATTTGCATTAGAGTCCTCATCACACAGGTACTGATGGATAAGACAGGGGAGCGTTTGCAAAAGATTTGTGAGTGGAGATTTTTCTGAGCTCTTTGTCTTAATGGATCGCAGCAGTTCATGGGACCCTTCCTCAGCTTCATCATCAAACAAAAAAAAAATCAAGTTGCGAAGTATATATAATTTGTTTTTTTGTTTGGATTTTTAAGATTTTTGATTCCTTGTGTGTGACTTCACGTGACGGAGGCGTGTGTCTCACGTGTTTGTTTTCTCTTCAAATCTTTTATTTTGGCGGGAAATTTTGTGTTTTTGATTTCTACGTATTCGTGGACTCCAAATGAGTTTTGTCACGGTGCGTTTTAGTAGCGTTTGCATGCGTGTAAGGTGTCACGTATGTGTATATATATGATTTTTTTTTGGTTTCTTGAAAGGTTGAATTTTATAAATAAAACGTTTCTATTAT Coding sequence:MRSYRFSDYLHMSVSFSNDMDLFCGEDSGVFSGESTVDFSSSEVDSWPGDSIACFIEDERHFVPGHDYLSRFQTRSLDASAREDSVAWILKVQAYYNFQPLTAYLAVNYMDRFLYARRLPETSGWPMQLLAVACLSLAAKMEEILVPSLFDFQVAGVKYLFEAKTIKRMELLVLSVLDWRLRSVTPFDFISFFAYKIDPSGTFLGFFISHATEIILSNIKEASFLEYWPSSIAAAAILCVANELPSLSSVVNPHESPETWCDGLSKEKIVRCYRLMKAMAIENNRLNTPKVIAKLRVSVRASSTLTRPSDESSFSSSSPCKRRKLSGYSWVGDETSTSN* Microarray data shows that the coding sequence was expressed inthe following experiments, which shows that the promoter would be usefulto modulate expression in situations similar to the following: CDNA_IDSHORT_NAME EXPT_REP_ID IS_UP 13497447 At_Diversity_Expt 108457 −13497447 At_Diversity_Expt 108458 − 13497447 At_5-1-F2-137 108460 −13497447 At_Germinating_Seeds 108463 + 13497447 At_Germinating_Seeds108464 + 13497447 At_100uM_ABA_Mutants 20000069 − 13497447 At_42deg_Heat20000173 − 13497447 At_Open_Flower 20000286 + 13497447At_100uM_ABA_Mutants 20000573 − 13497447 At_100uM_ABA_Mutants 20000574 −13497447 At_Drought_Reproduction 20001906 − 13497447At_Drought_Reproduction 20001911 − 13497447 At_8deg_Cold 20002108 − Theparameters for the microarray experiments listed above by Expt_Rep_IDand Short_Name are as follow below: CDNA_ID SHORT_NAME EXPT_REP_IDPARAM_NAME VALUE 13497447 At_Diversity_Expt 108457 Plant Line Canola vs.WS 13497447 At_Diversity_Expt 108457 Tissue Hypocotyl 13497447At_Diversity_Expt 108458 Plant Line Holbolliie vs. WS 13497447At_Diversity_Expt 108458 Tissue Hypocotyl 13497447 At_5-1-F2-137 108460Plant Line 5-1-F2-137 (mutant) 13497447 At_5-1-F2-137 108460 ProbeMethod Amplified 13497447 At_5-1-F2-137 108460 Tissue Inflorescences13497447 At_Germinating_Seeds 108463 Age (day) 3 vs. 0 13497447At_Germinating_Seeds 108463 Tissue Germinating Seeds 13497447At_Germinating_Seeds 108464 Age (day) 4 vs. 0 13497447At_Germinating_Seeds 108464 Tissue Germinating Seeds 13497447At_100uM_ABA_Mutants 20000069 Timepoint (hr) 6 13497447At_100uM_ABA_Mutants 20000069 Treatment 100 uM ABA vs. No Treatment13497447 At_100uM_ABA_Mutants 20000069 Tissue Aerial 13497447At_100uM_ABA_Mutants 20000069 Plant Line CS23 13497447 At_42deg_Heat20000173 Timepoint (hr) 6 13497447 At_42deg_Heat 20000173 Age (day) 1413497447 At_42deg_Heat 20000173 Temperature (deg C.) 42 vs. 22 13497447At_42deg_Heat 20000173 Organism A. thaliana 13497447 At_42deg_Heat20000173 Tissue Aerial 13497447 At_42deg_Heat 20000173 Plant Line WS13497447 At_Open_Flower 20000286 Age (day) 21 13497447 At_Open_Flower20000286 Organism A. thaliana 13497447 At_Open_Flower 20000286 TissueHalf Open vs. Whole Plant 13497447 At_Open_Flower 20000286 Plant Line WS13497447 At_100uM_ABA_Mutants 20000573 Organism A. thaliana 13497447At_100uM_ABA_Mutants 20000573 Plant Line CS22 vs. Ler wt 13497447At_100uM_ABA_Mutants 20000573 Timepoint (hr) N/A 13497447At_100uM_ABA_Mutants 20000573 Treatment None 13497447At_100uM_ABA_Mutants 20000573 Tissue Whole Plant 13497447At_100uM_ABA_Mutants 20000574 Organism A. thaliana 13497447At_100uM_ABA_Mutants 20000574 Plant Line CS23 vs. Ler wt 13497447At_100uM_ABA_Mutants 20000574 Timepoint (hr) N/A 13497447At_100uM_ABA_Mutants 20000574 Treatment None 13497447At_100uM_ABA_Mutants 20000574 Tissue Whole Plant 13497447At_Drought_Reproduction 20001906 Timepoint (day) 5 13497447At_Drought_Reproduction 20001906 Age (day) 35 13497447At_Drought_Reproduction 20001906 Organism A. thaliana 13497447At_Drought_Reproduction 20001906 Treatment Drought vs. No Drought13497447 At_Drought_Reproduction 20001906 Tissue Siliques 13497447At_Drought_Reproduction 20001906 Plant Line WS 13497447At_Drought_Reproduction 20001911 Timepoint (day) 10 13497447At_Drought_Reproduction 20001911 Age (day) 40 13497447At_Drought_Reproduction 20001911 Organism A. thaliana 13497447At_Drought_Reproduction 20001911 Treatment Drought vs. No Drought13497447 At_Drought_Reproduction 20001911 Tissue Flowers 13497447At_Drought_Reproduction 20001911 Plant Line WS 13497447 At_8deg_Cold20002108 Age (day) 14 13497447 At_8deg_Cold 20002108 Timepoint (hr) 16813497447 At_8deg_Cold 20002108 Temperature (deg C.) 8 vs. 22 13497447At_8deg_Cold 20002108 Organism A. thaliana 13497447 At_8deg_Cold20002108 Tissue Whole Plant 13497447 At_8deg_Cold 20002108 Plant Line WSPromoter YP0377 Modulates the gene: product = “glycine-rich protein”,note: unknown protein The GenBank description of the gene::NM_100587Arabidopsis thaliana glycine-rich protein (At1g07135) mRNA, complete cdsgi|22329385|ref|NM_100587.2|[22329385] The promoter sequence:5′tttaaacataacaatgaattgcttggatttcaaactttattaaatttggattttaaattttaatttgattgaattatacccccttaattggataaattcaaatatgtcaactttttttttttgtaagatttttttatggaaaaaaaaattgattattcactaaaaagatgacaggttacttataatttaatatatgtaaaccctaaaaagaagaaaatagtttctgttttcactttaggtcttattatctaaacttctttaagaaaatcgcaataaattggtttgagttctaactttaaacacattaatatttgtgtgctatttaaaaaataatttacaaaaaaaaaaacaaattgacagaaaatatcaggttttgtaataagatatttcctgataaatatttagggaatataacatatcaaaagattcaaattctgaaaatcaagaatggtagacatgtgaaagttgtcatcaatatggtccacttttctttgctctataacccaaaattgaccctgacagtcaacttgtacacgcggccaaacctttttataatcatgctatttatttccttcatttttattctatttgctatctaactgatttttcattaacatgataccagaaatgaatttagatggattaattcttttccatccacgacatctggaaacacttatctcctaattaaccttactttttttttagtttgtgtgctccttcataaaatctatattgtttaaaacaaaggtcaataaatataaatatggataagtataataaatctttattggatatttctttttttaaaaaagaaataaatcttttttggatattttcgtggcagcatcataatgagagactacgtcgaaactgctggcaaccacttttgccgcgtttaatttctttctgaggcttatataaatagatcaaaggggaaagtgagaTAT 3′ The promoter was cloned from theorganism: Arabidopsis thaliana, Columbia ecotype Alternativenucleotides: Predicted Position (bp) Mismatch Predicted/Experimental 145Sequence or PCR error ctttttttttttg/ ctttttttt-ttg Exp. 1 ctttttttt--tgExp. 2 The promoter was cloned in the vector: pNewbin4-HAP1-GFP Whencloned into the vector the promoter was operably linked to a marker,which was the type: GFP-ER Promoter-marker vector was tested in:Arabidopsis thaliana, WS ecotype Generation screened: XT1 Mature   XT2Seedling   T2 Mature   T3 Seedling The spatial expression of thepromoter-marker vector was found observed in and would be useful inexpression in any or all of the following: Flower M sepal M petal Mepidermis Hypocotyl L epidermis L vascular H stomata Cotyledon Mvascular L epidermis Primary Root M epidermis M vascular M root hairsObserved expression pattern of the promoter-marker vector was in: T1mature: Expressed in epidermal cells of sepals and petals in developingflowers. T2 seedling: Medium to low expression in epidermal and vascularcells of hypocotyls and cotyledons. Epidermal and vascular expression atroot transition zone decreasing toward root tip. Misc. promoterinformation:   Bidirectionality: Pass   Exons: Pass    Repeats: No TheCeres cDNA ID of the endogenous coding sequence to the promoter:13613778 cDNA nucleotide sequence:AAAGAAAATGGGTTTGAGAAGAACATGGTTGGTTTTGTACATTCTCTTCATCTTTCATCTTCAGCACAATCTTCCTTCCGTGAGCTCACGACCTTCCTCAGTCGATACAAACCACGAGACTCTCCCTTTTAGTGTTTCAAAGCCAGACGTTGTTGTGTTTGAAGGAAAGGCTCGGGAATTAGCTGTCGTTATCAAAAAAGGAGGAGGTGGAGGAGGTGGAGGACGCGGAGGCGGTGGAGCACGAAGCGGCGGTAGGAGCAGGGGAGGAGGAGGTGGCAGCAGTAGTAGCCGCAGCCGTGACTGGAAACGCGGCGGAGGGGTGGTTCCGATTCATACGGGTGGTGGTAATGGCAGTCTGGGTGGTGGATCGGCAGGATCACATAGATCAAGCGGCAGCATGAATCTTCGAGGAACAATGTGTGCGGTCTGTTGGTTGGCTTTATCGGTTTTAGCCGGTTTAGTCTTGGTTCAGTAGGGTTCAGAGTAATTATTGGCCATTTATTTATTGGTTTTGTAACGTTTATGTTTGTGGTCCGGTCTGATATTTATTTGGGCAAACGGTACATTAAGGTGTAGACTGTTAATATTATATGTAGAAAGAGATTCTTAGCAGGATTCTACTGGTAGTATTAAGAGTGAGTTATCTTTAGTATGCCATTTGTAAATGGAAATTTAATGAAATAAGAAATTGTGAAATTTAAAC Coding sequence:KKMGLRRTWLVLYILFIFHLQHNLPSVSSRPSSVDTNHETLPFSVSKPDVVVFEGKARELAVVIKKGGGGGGGGRGGGGARSGGRSRGGGGGSSSSRSRDWKRGGGVVPIHTGGGNGSLGGGSAGSHRSSGSMNLRGTMCAVCWLALSVLAGLVLVQ* Microarray data shows that thecoding sequence was expressed in the following experiments, which showsthat the promoter would be useful to modulate expression in situationssimilar to the following: CDNA_ID SHORT_NAME EXPT_REP_ID IS_UP 13613778At_Root_Tips 108434 − 13613778 At_20uM_KNO3_H-to-L 108455 + 13613778At_5-1-F2-137 108460 + 13613778 At_Germinating_Seeds 108464 + 13613778At_Shoot_Apices 108480 + 13613778 At_Shoot_Apices 108481 + 13613778At_15mM_NH4NO3_L-to-H_Rosette 108487 − 13613778At_15mM_NH4NO3_L-to-H_Rosette 108488 − 13613778 At_ap2_floral_buds108501 − 13613778 At_42deg_Heat 108577 − 13613778 At_4deg_Cold 108578 +13613778 At_4deg_Cold 108579 + 13613778 At_5mM_NaNP 108584 + 13613778At_5mM_NaNP 108585 + 13613778 At_2mM_SA 108586 − 13613778 At_2mM_SA108587 − 13613778 At_15mM_NH4NO3_L-to-H 108588 + 13613778At_Ler-pi_Ovule 108595 + 13613778 At_100uM_ABA 108606 − 13613778At_2mM_SA 108667 + 13613778 At_100uM_ABA_Mutants 20000069 + 13613778At_100uM_ABA_Mutants 20000071 + 13613778 At_100uM_ABA_Mutants 20000086 +13613778 At_100uM_ABA_Mutants 20000087 + 13613778At_2mM_SA_CS3726-Columbia 20000091 + 13613778 At_100uM_ABA_Mutants20000117 + 13613778 At_42deg_Heat 20000144 − 13613778 At_42deg_Heat20000171 − 13613778 At_42deg_Heat 20000173 − 13613778 At_2mM_SA20000181 + 13613778 At_Shoots 20000184 − 13613778 At_Roots 20000185 −13613778 At_4deg_Cold 20000213 + 13613778 At_Siliques 20000234 −13613778 At_Siliques 20000236 − 13613778 At_Open_Flower 20000264 −13613778 At_100mM_NaCl 20000268 − 13613778 At_Open_Flower 20000286 −13613778 At_Pollen 20000326 − 13613778 At_Shoots 20000438 − 13613778At_Roots 20000439 − 13613778 At_1uM_BR-BRZ 20000441 + 13613778At_1uM_BR-BRZ 20000443 + 13613778 At_42deg_Heat 20000458 − 13613778At_10percent_PEG 20000460 + 13613778 At_Guard_Cells 20000495 − 13613778At_10percent_PEG 20000527 + 13613778 At_100uM_ABA_Mutants 20000573 −13613778 At_100uM_ABA_Mutants 20000574 − 13613778 At_Herbicide_Mutants20000640 − 13613778 At_15mM_NH4NO3_L-to-H 20000709 + 13613778 At_Petals20000794 − 13613778 At_Line_Comparisons 20001151 − 13613778At_Line_Comparisons 20001184 − 13613778 At_Line_Comparisons 20001192 −13613778 At_Line_Comparisons 20001195 − 13613778 At_Far-red-induction20001247 + 13613778 At_Far-red-induction 20001248 + 13613778At_Line_Comparisons 20001300 − 13613778 At_Line_Comparisons 20001307 −13613778 At_Line_Comparisons 20001308 + 13613778 At_Line_Comparisons20001309 + 13613778 At_Line_Comparisons 20001310 + 13613778At_Line_Comparisons 20001318 − 13613778 At_Line_Comparisons 20001319 −13613778 At_Line_Comparisons 20001347 − 13613778 At_Line_Comparisons20001448 − 13613778 At_50mM_NH4NO3_L-to-H 20001458 + 13613778At_Drought_Soil_Dry 20001554 − 13613778 At_Drought_Soil_Dry 20001555 −13613778 At_Drought_Soil_Dry 20001556 − 13613778 At_Drought_Soil_Dry20001557 + 13613778 At_Interploidy_Crosses 20001703 − 13613778At_50mM_NH4NO3_L-to-H 20001757 − 13613778 At_Far-red-enriched-adult20001773 − 13613778 At_Far-red-enriched-adult 20001774 − 13613778At_Drought_Reproduction 20001904 − 13613778 At_Drought_Reproduction20001907 − 13613778 At_Line_Comparisons 20002012 + 13613778 At_8deg_Cold20002108 − 13613778 At_8deg_Cold 20002109 − The parameters for themicroarray experiments listed above by Expt_Rep_ID and Short_Name are asfollow below: CDNA_ID SHORT_NAME EXPT_REP_ID PARAM_NAME VALUE 13613778At_Root_Tips 108434 Tissue Root Tips 13613778 At_20uM_KNO3_H-to-L 108455Timepoint (hr) 1 13613778 At_20uM_KNO3_H-to-L 108455 Treatment 20 uMKNO3 vs. 50 mM KNO3 13613778 At_5-1-F2-137 108460 Plant Line 5-1-F2-137(mutant) 13613778 At_5-1-F2-137 108460 Probe Method Amplified 13613778At_5-1-F2-137 108460 Tissue Inflorescences 13613778 At_Germinating_Seeds108464 Age (day) 4 vs. 0 13613778 At_Germinating_Seeds 108464 TissueGerminating Seeds 13613778 At_Shoot_Apices 108480 Treatment 1 uM BR vs.No Treatment 13613778 At_Shoot_Apices 108480 Plant Line Ws-2 13613778At_Shoot_Apices 108481 Treatment 1 uM BRZ vs. No Treatment 13613778At_Shoot_Apices 108481 Plant Line Ws-2 13613778 At_15mM_NH4NO3_L-to-108487 Timepoint (hr) 0.5 H_Rosette 13613778 At_15mM_NH4NO3_L-to- 108487Treatment 15 mM NH4NO3 vs. 30 mM Mannitol H_Rosette 13613778At_15mM_NH4NO3_L-to- 108487 Tissue Rosette H_Rosette 13613778At_15mM_NH4NO3_L-to- 108488 Timepoint (hr) 2 H_Rosette 13613778At_15mM_NH4NO3_L-to- 108488 Treatment 15 mM NH4NO3 vs. 30 mM MannitolH_Rosette 13613778 At_15mM_NH4NO3_L-to- 108488 Tissue Rosette H_Rosette13613778 At_ap2_floral_buds 108501 Plant Line ap2 (Ler.) 13613778At_ap2_floral_buds 108501 Tissue Closed Flower 13613778 At_42deg_Heat108577 Timepoint (hr) 6 13613778 At_42deg_Heat 108577 Temperature 42 vs.22 (deg C.) 13613778 At_42deg_Heat 108577 Tissue Aerial 13613778At_4deg_Cold 108578 Timepoint (hr) 1 13613778 At_4deg_Cold 108578Temperature 4 vs. 22 (deg C.) 13613778 At_4deg_Cold 108578 Tissue Aerial13613778 At_4deg_Cold 108579 Timepoint (hr) 6 13613778 At_4deg_Cold108579 Temperature 4 vs. 22 (deg C.) 13613778 At_4deg_Cold 108579 TissueAerial 13613778 At_5mM_NaNP 108584 Timepoint (hr) 1 13613778 At_5mM_NaNP108584 Treatment 5 mM sodium nitroprusside vs. No Treatment 13613778At_5mM_NaNP 108584 Tissue Aerial 13613778 At_5mM_NaNP 108585 Timepoint(hr) 6 13613778 At_5mM_NaNP 108585 Treatment 5 mM sodium nitroprussidevs. No Treatment 13613778 At_5mM_NaNP 108585 Tissue Aerial 13613778At_2mM_SA 108586 Timepoint (hr) 1 13613778 At_2mM_SA 108586 Treatment 2mM SA vs. No Treatment 13613778 At_2mM_SA 108586 Tissue Aerial 13613778At_2mM_SA 108587 Timepoint (hr) 6 13613778 At_2mM_SA 108587 Treatment 2mM SA vs. No Treatment 13613778 At_2mM_SA 108587 Tissue Aerial 13613778At_15mM_NH4NO3_L-to-H 108588 Timepoint (hr) 2 13613778At_15mM_NH4NO3_L-to-H 108588 Treatment 15 mM NH4NO3 vs. 30 mM Mannitol13613778 At_15mM_NH4NO3_L-to-H 108588 Tissue Aerial 13613778At_Ler-pi_Ovule 108595 Plant Line Ler_pi 13613778 At_Ler-pi_Ovule 108595Tissue Ovules 13613778 At_100uM_ABA 108606 Timepoint (hr) 2 13613778At_100uM_ABA 108606 Treatment 100 uM ABA vs. No Treatment 13613778At_100uM_ABA 108606 Tissue Aerial 13613778 At_2mM_SA 108667 Timepoint(hr) 1 13613778 At_2mM_SA 108667 Treatment 2 mM SA vs. No Treatment13613778 At_2mM_SA 108667 Plant Line WS 13613778 At_100uM_ABA_Mutants20000069 Timepoint (hr) 6 13613778 At_100uM_ABA_Mutants 20000069Treatment 100 uM ABA vs. No Treatment 13613778 At_100uM_ABA_Mutants20000069 Tissue Aerial 13613778 At_100uM_ABA_Mutants 20000069 Plant LineCS23 13613778 At_100uM_ABA_Mutants 20000071 Timepoint (hr) 6 13613778At_100uM_ABA_Mutants 20000071 Treatment 100 uM ABA vs. No Treatment13613778 At_100uM_ABA_Mutants 20000071 Tissue Aerial 13613778At_100uM_ABA_Mutants 20000071 Plant Line CS8104 13613778At_100uM_ABA_Mutants 20000086 Timepoint (hr) 6 13613778At_100uM_ABA_Mutants 20000086 Treatment 100 uM ABA vs. No Treatment13613778 At_100uM_ABA_Mutants 20000086 Tissue Aerial 13613778At_100uM_ABA_Mutants 20000086 Plant Line CS22 13613778At_100uM_ABA_Mutants 20000087 Timepoint (hr) 6 13613778At_100uM_ABA_Mutants 20000087 Treatment 100 uM ABA vs. No Treatment13613778 At_100uM_ABA_Mutants 20000087 Tissue Aerial 13613778At_100uM_ABA_Mutants 20000087 Plant Line WS 13613778 At_2mM_SA_CS3726-20000091 Timepoint (hr) 0 Columbia 13613778 At_2mM_SA_CS3726- 20000091Tissue Aerial Columbia 13613778 At_2mM_SA_CS3726- 20000091 Plant LineCS3726 vs. Columbia Columbia 13613778 At_2mM_SA_CS3726- 20000091Treatment None Columbia 13613778 At_100uM_ABA_Mutants 20000117 Timepoint(hr) 6 13613778 At_100uM_ABA_Mutants 20000117 Treatment 100 uM ABA vs.No Treatment 13613778 At_100uM_ABA_Mutants 20000117 Tissue Aerial13613778 At_100uM_ABA_Mutants 20000117 Plant Line Columbia 13613778At_42deg_Heat 20000144 Timepoint (hr) 1 13613778 At_42deg_Heat 20000144Temperature 42 vs. 22 (deg C.) 13613778 At_42deg_Heat 20000144 TissueAerial 13613778 At_42deg_Heat 20000171 Timepoint (hr) 1 13613778At_42deg_Heat 20000171 Age (day) 14 13613778 At_42deg_Heat 20000171Temperature 42 vs. 22 (deg C.) 13613778 At_42deg_Heat 20000171 OrganismA. thaliana 13613778 At_42deg_Heat 20000171 Tissue Aerial 13613778At_42deg_Heat 20000171 Plant Line WS 13613778 At_42deg_Heat 20000173Timepoint (hr) 6 13613778 At_42deg_Heat 20000173 Age (day) 14 13613778At_42deg_Heat 20000173 Temperature 42 vs. 22 (deg C.) 13613778At_42deg_Heat 20000173 Organism A. thaliana 13613778 At_42deg_Heat20000173 Tissue Aerial 13613778 At_42deg_Heat 20000173 Plant Line WS13613778 At_2mM_SA 20000181 Timepoint (hr) 1 13613778 At_2mM_SA 20000181Age (day) 14 13613778 At_2mM_SA 20000181 Treatment 2 mM SA vs. NoTreatment 13613778 At_2mM_SA 20000181 Organism A. thaliana 13613778At_2mM_SA 20000181 Tissue Aerial 13613778 At_2mM_SA 20000181 Plant LineWS 13613778 At_Shoots 20000184 Age (day) 7 vs. 21 13613778 At_Shoots20000184 Organism A. thaliana 13613778 At_Shoots 20000184 Tissue Shootsvs. Whole Plant 13613778 At_Shoots 20000184 Plant Line WS 13613778At_Roots 20000185 Age (day) 7 vs. 21 13613778 At_Roots 20000185 OrganismA. thaliana 13613778 At_Roots 20000185 Tissue Roots vs. Whole Plant13613778 At_Roots 20000185 Plant Line WS 13613778 At_4deg_Cold 20000213Timepoint (hr) 2 13613778 At_Siliques 20000234 Age (day) 21 13613778At_Siliques 20000234 Tissue <5 mm Siliques vs. Whole Plant 13613778At_Siliques 20000234 Organism A. thaliana 13613778 At_Siliques 20000234Plant Line WS 13613778 At_Siliques 20000236 Age (day) 21 13613778At_Siliques 20000236 Tissue >10 mm Siliques vs. Whole Plant 13613778At_Siliques 20000236 Organism A. thaliana 13613778 At_Siliques 20000236Plant Line WS 13613778 At_Open_Flower 20000264 Age (day) 21 13613778At_Open_Flower 20000264 Organism A. thaliana 13613778 At_Open_Flower20000264 Tissue Open Flower vs. Whole Plant 13613778 At_Open_Flower20000264 Plant Line WS 13613778 At_100mM_NaCl 20000268 Timepoint (hr) 613613778 At_100mM_NaCl 20000268 Age (day) 14 13613778 At_100mM_NaCl20000268 Treatment 100 mM NaCl vs. No Treatment 13613778 At_100mM_NaCl20000268 Organism A. thaliana 13613778 At_100mM_NaCl 20000268 TissueWhole Plant 13613778 At_100mM_NaCl 20000268 Plant Line WS 13613778At_Open_Flower 20000286 Age (day) 21 13613778 At_Open_Flower 20000286Organism A. thaliana 13613778 At_Open_Flower 20000286 Tissue Half Openvs. Whole Plant 13613778 At_Open_Flower 20000286 Plant Line WS 13613778At_Pollen 20000326 Age (day) 0 vs. 21 13613778 At_Pollen 20000326Organism A. thaliana 13613778 At_Pollen 20000326 Tissue Pollen vs. WholePlant 13613778 At_Pollen 20000326 Plant Line WS 13613778 At_Shoots20000438 Age (day) 14 vs. 21 13613778 At_Shoots 20000438 Organism A.thaliana 13613778 At_Shoots 20000438 Tissue Shoots vs. Whole Plant13613778 At_Shoots 20000438 Plant Line WS 13613778 At_Roots 20000439 Age(day) 14 vs. 21 13613778 At_Roots 20000439 Organism A. thaliana 13613778At_Roots 20000439 Tissue Roots vs. Whole Plant 13613778 At_Roots20000439 Plant Line WS 13613778 At_1uM_BR-BRZ 20000441 Treatment 1 uM BRvs. No Treatment 13613778 At_1uM_BR-BRZ 20000441 Tissue Shoot Apices13613778 At_1uM_BR-BRZ 20000443 Treatment 1 uM BRZ vs. No Treatment13613778 At_1uM_BR-BRZ 20000443 Tissue Shoot Apices 13613778At_42deg_Heat 20000458 Timepoint (hr) 8 13613778 At_42deg_Heat 20000458Age (day) 14 13613778 At_42deg_Heat 20000458 Temperature 42 vs. 22 (degC.) 13613778 At_42deg_Heat 20000458 Organism A. thaliana 13613778At_42deg_Heat 20000458 Tissue Aerial 13613778 At_42deg_Heat 20000458Plant Line WS 13613778 At_10percent_PEG 20000460 Age (day) 12 13613778At_10percent_PEG 20000460 Timepoint (day) 12 13613778 At_10percent_PEG20000460 Treatment 10 percent PEG vs. No Treatment 13613778At_10percent_PEG 20000460 Organism A. thaliana 13613778 At_10percent_PEG20000460 Tissue Whole Plant 13613778 At_10percent_PEG 20000460 PlantLine WS 13613778 At_Guard_Cells 20000495 Harvest Date 08 Feb. 200213613778 At_Guard_Cells 20000495 Organism A. thaliana 13613778At_Guard_Cells 20000495 Tissue Guard Cells vs. Leaves 13613778At_10percent_PEG 20000527 Age (day) 20 13613778 At_10percent_PEG20000527 Timepoint (day) 20 13613778 At_10percent_PEG 20000527 Treatment10 percent PEG vs. No Treatment 13613778 At_10percent_PEG 20000527Organism A. thaliana 13613778 At_10percent_PEG 20000527 Tissue WholePlant 13613778 At_10percent_PEG 20000527 Plant Line WS 13613778At_100uM_ABA_Mutants 20000573 Organism A. thaliana 13613778At_100uM_ABA_Mutants 20000573 Plant Line CS22 vs. Ler wt 13613778At_100uM_ABA_Mutants 20000573 Timepoint (hr) N/A 13613778At_100uM_ABA_Mutants 20000573 Treatment None 13613778At_100uM_ABA_Mutants 20000573 Tissue Whole Plant 13613778At_100uM_ABA_Mutants 20000574 Organism A. thaliana 13613778At_100uM_ABA_Mutants 20000574 Plant Line CS23 vs. Ler wt 13613778At_100uM_ABA_Mutants 20000574 Timepoint (hr) N/A 13613778At_100uM_ABA_Mutants 20000574 Treatment None 13613778At_100uM_ABA_Mutants 20000574 Tissue Whole Plant 13613778At_Herbicide_Mutants 20000640 Timepoint (hr) 12 13613778At_Herbicide_Mutants 20000640 Plant Line 05377RR/BR27173 13613778At_Herbicide_Mutants 20000640 Treatment Roundup vs. No Treatment13613778 At_Herbicide_Mutants 20000640 Tissue Seedlings 13613778At_15mM_NH4NO3_L-to-H 20000709 Timepoint (hr) 4 13613778At_15mM_NH4NO3_L-to-H 20000709 Age (hr) 14 13613778At_15mM_NH4NO3_L-to-H 20000709 Treatment 15 mM NH4NO3 vs. 30 mM Mannitol13613778 At_15mM_NH4NO3_L-to-H 20000709 Organism A. thaliana 13613778At_15mM_NH4NO3_L-to-H 20000709 Tissue Aerial 13613778At_15mM_NH4NO3_L-to-H 20000709 Plant Line WS 13613778 At_Petals 20000794Age (day) 23-25 days 13613778 At_Petals 20000794 Organism A. thaliana13613778 At_Petals 20000794 Tissue Petals vs. Whole plant 13613778At_Petals 20000794 Plant Line WS 13613778 At_Line_Comparisons 20001151Plant Line ME01339-01 vs. WS 13613778 At_Line_Comparisons 20001184 PlantLine ME01848-01 vs. WS 13613778 At_Line_Comparisons 20001192 Plant LineWBin4-WX13R-A vs. WS 13613778 At_Line_Comparisons 20001195 Plant LineWBin4-WX14-B vs. WS 13613778 At_Far-red-induction 20001247 Timepoint(hr) 1 13613778 At_Far-red-induction 20001247 Age (day) 7 13613778At_Far-red-induction 20001247 Organism A. thaliana 13613778At_Far-red-induction 20001247 Plant Line Columbia 13613778At_Far-red-induction 20001247 Light Far-red vs. White 13613778At_Far-red-induction 20001247 Tissue Whole Plant 13613778At_Far-red-induction 20001248 Timepoint (hr) 4 13613778At_Far-red-induction 20001248 Age (day) 7 13613778 At_Far-red-induction20001248 Organism A. thaliana 13613778 At_Far-red-induction 20001248Plant Line Columbia 13613778 At_Far-red-induction 20001248 Light Far-redvs. White 13613778 At_Far-red-induction 20001248 Tissue Whole Plant13613778 At_Line_Comparisons 20001300 Plant Line ME01338-05 vs. WS13613778 At_Line_Comparisons 20001307 Plant Line WBin4-WX2-A vs. WS13613778 At_Line_Comparisons 20001308 Plant Line WBin4-WX49-C vs. WS13613778 At_Line_Comparisons 20001309 Plant Line WBin4-WX49R-A vs. WS13613778 At_Line_Comparisons 20001310 Plant Line WBin4-WX17-A vs. WS13613778 At_Line_Comparisons 20001318 Plant Line WBin4-WX14R-A vs. WS13613778 At_Line_Comparisons 20001319 Plant Line WBin4-WX24-A vs. WS13613778 At_Line_Comparisons 20001347 Plant Line ME01604-01 vs. WS13613778 At_Line_Comparisons 20001448 Plant Line ME01323-01 vs. WS13613778 At_50mM_NH4NO3_L-to-H 20001458 Timepoint (hr) 2 13613778At_50mM_NH4NO3_L-to-H 20001458 Treatment 50 mM NH4NO3 vs. 100 mM Manitol13613778 At_50mM_NH4NO3_L-to-H 20001458 Organism A. thaliana 13613778At_50mM_NH4NO3_L-to-H 20001458 Tissue Siliques 13613778At_50mM_NH4NO3_L-to-H 20001458 Age (day) Undefined 13613778At_50mM_NH4NO3_L-to-H 20001458 Plant Line WS 13613778At_Drought_Soil_Dry 20001554 Timepoint (day) 7 13613778At_Drought_Soil_Dry 20001554 Age (day) 21 13613778 At_Drought_Soil_Dry20001554 Organism A. thaliana 13613778 At_Drought_Soil_Dry 20001554Treatment Drought vs. No Drought 13613778 At_Drought_Soil_Dry 20001554Post Timepoint None (hr) 13613778 At_Drought_Soil_Dry 20001554Post-Treatment None 13613778 At_Drought_Soil_Dry 20001554 Plant Line WS13613778 At_Drought_Soil_Dry 20001555 Timepoint (day) 10 13613778At_Drought_Soil_Dry 20001555 Age (day) 24 13613778 At_Drought_Soil_Dry20001555 Organism A. thaliana 13613778 At_Drought_Soil_Dry 20001555Treatment Drought vs. No Drought 13613778 At_Drought_Soil_Dry 20001555Post Timepoint None (hr) 13613778 At_Drought_Soil_Dry 20001555Post-Treatment None 13613778 At_Drought_Soil_Dry 20001555 Plant Line WS13613778 At_Drought_Soil_Dry 20001556 Timepoint (day) 12 13613778At_Drought_Soil_Dry 20001556 Age (day) 26 13613778 At_Drought_Soil_Dry20001556 Organism A. thaliana 13613778 At_Drought_Soil_Dry 20001556Treatment Drought vs. No Drought 13613778 At_Drought_Soil_Dry 20001556Post Timepoint None (hr) 13613778 At_Drought_Soil_Dry 20001556Post-Treatment None 13613778 At_Drought_Soil_Dry 20001556 Plant Line WS13613778 At_Drought_Soil_Dry 20001557 Post Timepoint 3 (hr) 13613778At_Drought_Soil_Dry 20001557 Timepoint (day) 13 13613778At_Drought_Soil_Dry 20001557 Age (day) 27 13613778 At_Drought_Soil_Dry20001557 Organism A. thaliana 13613778 At_Drought_Soil_Dry 20001557Treatment Drought vs. No Drought 13613778 At_Drought_Soil_Dry 20001557Post-Treatment Re-Water vs. No Drought 13613778 At_Drought_Soil_Dry20001557 Plant Line WS 13613778 At_Interploidy_Crosses 20001703 Age(day) 5 13613778 At_Interploidy_Crosses 20001703 Cross 2X × 4X vs. 2X× 2X 13613778 At_Interploidy_Crosses 20001703 Organism A. thaliana13613778 At_Interploidy_Crosses 20001703 Plant Line Columbia 13613778At_Interploidy_Crosses 20001703 Tissue Siliques 13613778At_50mM_NH4NO3_L-to-H 20001757 Timepoint (hr) 6 13613778At_50mM_NH4NO3_L-to-H 20001757 Treatment 50 mM NH4NO3 vs 100 mM Mannitol13613778 At_50mM_NH4NO3_L-to-H 20001757 Tissue Leaf 13613778At_Far-red-enriched-adult 20001773 Age (day) 30 13613778At_Far-red-enriched-adult 20001773 Timepoint (hr) 48 13613778At_Far-red-enriched-adult 20001773 Organism A. thaliana 13613778At_Far-red-enriched-adult 20001773 Tissue Aerial 13613778At_Far-red-enriched-adult 20001773 Plant Line Columbia 13613778At_Far-red-enriched-adult 20001773 Light Far-red enriched vs. White13613778 At_Far-red-enriched-adult 20001774 Age (day) 31 13613778At_Far-red-enriched-adult 20001774 Timepoint (hr) 72 13613778At_Far-red-enriched-adult 20001774 Organism A. thaliana 13613778At_Far-red-enriched-adult 20001774 Tissue Aerial 13613778At_Far-red-enriched-adult 20001774 Plant Line Columbia 13613778At_Far-red-enriched-adult 20001774 Light Far-red enriched vs. White13613778 At_Drought_Reproduction 20001904 Timepoint (day) 7 13613778At_Drought_Reproduction 20001904 Age (day) 37 13613778At_Drought_Reproduction 20001904 Organism A. thaliana 13613778At_Drought_Reproduction 20001904 Treatment Drought vs. No Drought13613778 At_Drought_Reproduction 20001904 Tissue Rosettes 13613778At_Drought_Reproduction 20001904 Plant Line WS 13613778At_Drought_Reproduction 20001907 Timepoint (day) 7 13613778At_Drought_Reproduction 20001907 Age (day) 37 13613778At_Drought_Reproduction 20001907 Organism A. thaliana 13613778At_Drought_Reproduction 20001907 Treatment Drought vs. No Drought13613778 At_Drought_Reproduction 20001907 Tissue Siliques 13613778At_Drought_Reproduction 20001907 Plant Line WS 13613778At_Line_Comparisons 20002012 Plant Line SALK_073455 vs. Columbia13613778 At_8deg_Cold 20002108 Age (day) 14 13613778 At_8deg_Cold20002108 Timepoint (hr) 168 13613778 At_8deg_Cold 20002108 Temperature 8vs. 22 (deg C.) 13613778 At_8deg_Cold 20002108 Organism A. thaliana13613778 At_8deg_Cold 20002108 Tissue Whole Plant 13613778 At_8deg_Cold20002108 Plant Line WS 13613778 At_8deg_Cold 20002109 Age (day) 1613613778 At_8deg_Cold 20002109 Timepoint (hr) 216 13613778 At_8deg_Cold20002109 Temperature 8 vs. 22 (deg C.) 13613778 At_8deg_Cold 20002109Organism A. thaliana 13613778 At_8deg_Cold 20002109 Tissue Whole Plant13613778 At_8deg_Cold 20002109 Plant Line WS

TABLE 2 Promoter Utilities Based on Differential Expression ExperimentsEXPT_REP_ID SHORT_NAME UTILITY 20000166 At_100uM_ABA Promoters and cDNAscorresponding to endogenous cDNAs which were differentially expressed inthis experiment would be useful in modulating ABA, stress, and droughtinduced and/or regulated responses 20000169 At_100uM_ABA Promoters andcDNAs corresponding to endogenous cDNAs which were differentiallyexpressed in this experiment would be useful in modulating ABA, stress,and drought induced and/or regulated responses 20000171 At_42deg_HeatPromoters and cDNAs corresponding to endogenous cDNAs which weredifferentially expressed in this experiment would be useful inmodulating stress, heat and cold induced and/or regulated responses20000173 At_42deg_Heat Promoters and cDNAs corresponding to endogenouscDNAs which were differentially expressed in this experiment would beuseful in modulating stress, heat and cold induced and/or regulatedresponses 20000179 At_Germinating_Seeds Promoters and cDNAscorresponding to endogenous cDNAs which were differentially expressed inthis experiment would be useful for modulating growth, yield and plantdevelopment 20000180 At_Germinating_Seeds Promoters and cDNAscorresponding to endogenous cDNAs which were differentially expressed inthis experiment would be useful for modulating growth, yield and plantdevelopment 20000182 At_2mM_SA Promoters and cDNAs corresponding toendogenous cDNAs which were differentially expressed in this experimentwould be useful in modulating stress and SA induced and/or regulatedresponses 20000184 At_Shoots Promoters and cDNAs corresponding toendogenous cDNAs which were differentially expressed in this experimentwould be useful for modulating growth, yield, and plant development forinstance in roots and/or shoots 20000185 At_Roots Promoters and cDNAscorresponding to endogenous cDNAs which were differentially expressed inthis experiment would be useful for modulating growth, yield, and plantdevelopment for instance in roots and/or shoots 20000227At_Root-Tips-vs-Tops Promoters and cDNAs corresponding to endogenouscDNAs which were differentially expressed in this experiment would beuseful for modulating growth, yield, and plant development for instancein roots and/or shoots 20000234 At_Siliques Promoters and cDNAscorresponding to endogenous cDNAs which were differentially expressed inthis experiment would be useful for modulating fertility, fruit and seedsize, number and/or yield 20000235 At_Siliques Promoters and cDNAscorresponding to endogenous cDNAs which were differentially expressed inthis experiment would be useful for modulating fertility, fruit and seedsize, number and/or yield 20000264 At_Open_Flower Promoters and cDNAscorresponding to endogenous cDNAs which were differentially expressed inthis experiment would be useful for modulating fertility, fruit and seedsize, number and/or yield, including flowers development and number20000265 At_Open_Flower Promoters and cDNAs corresponding to endogenouscDNAs which were differentially expressed in this experiment would beuseful for modulating fertility, fruit and seed size, number and/oryield, including flowers development and number 20000267 At_DroughtPromoters and cDNAs corresponding to endogenous cDNAs which weredifferentially expressed in this experiment would be useful formodulating stress and drought tolerance 20000286 At_Open_FlowerPromoters and cDNAs corresponding to endogenous cDNAs which weredifferentially expressed in this experiment would be useful formodulating fertility, fruit and seed size, number and/or yield,including flowers development and number 20000436 At_Drought Promotersand cDNAs corresponding to endogenous cDNAs which were differentiallyexpressed in this experiment would be useful for modulating stress anddrought tolerance 20000437 At_Drought Promoters and cDNAs correspondingto endogenous cDNAs which were differentially expressed in thisexperiment would be useful for modulating stress and drought tolerance20000438 At_Shoots Promoters and cDNAs corresponding to endogenous cDNAswhich were differentially expressed in this experiment would be usefulfor modulating growth, yield, and plant development for instance inroots and/or shoots 20000439 At_Roots Promoters and cDNAs correspondingto endogenous cDNAs which were differentially expressed in thisexperiment would be useful for modulating growth, yield, and plantdevelopment for instance in roots and/or shoots 20000441 At_1uM_BR-BRZPromoters and cDNAs corresponding to endogenous cDNAs which weredifferentially expressed in this experiment would be useful formodulating growth, yield and BR induced and/regulated responses 20000443At_1uM_BR-BRZ Promoters and cDNAs corresponding to endogenous cDNAswhich were differentially expressed in this experiment would be usefulfor modulating growth, yield and BR induced and/regulated responses20000451 At_CS6879_Shoots-Roots Promoters and cDNAs corresponding toendogenous cDNAs which were differentially expressed in this experimentwould be useful for modulating growth, yield, and plant development forinstance in roots and/or shoots 20000453 At_100uM_ABA Promoters andcDNAs corresponding to endogenous cDNAs which were differentiallyexpressed in this experiment would be useful in modulating ABA, stress,and drought induced and/or regulated responses 20000457 At_42deg_HeatPromoters and cDNAs corresponding to endogenous cDNAs which weredifferentially expressed in this experiment would be useful inmodulating stress, heat and cold induced and/or regulated responses20000458 At_42deg_Heat Promoters and cDNAs corresponding to endogenouscDNAs which were differentially expressed in this experiment would beuseful in modulating stress, heat and cold induced and/or regulatedresponses 20000460 At_10percent_PEG Promoters and cDNAs corresponding toendogenous cDNAs which were differentially expressed in this experimentwould be useful for modulating stress, drought tolerance, and osmoticstress 20000495 At_Guard_Cells Promoters and cDNAs corresponding toendogenous cDNAs which were differentially expressed in this experimentwould be useful for modulating guard cells, drought and stress tolerance20000527 At_10percent_PEG Promoters and cDNAs corresponding toendogenous cDNAs which were differentially expressed in this experimentwould be useful for modulating stress, drought tolerance, and osmoticstress 20000573 At_100uM_ABA_Mutants Promoters and cDNAs correspondingto endogenous cDNAs which were differentially expressed in thisexperiment would be useful in modulating ABA, stress, and droughtinduced and/or regulated responses 20000574 At_100uM_ABA_MutantsPromoters and cDNAs corresponding to endogenous cDNAs which weredifferentially expressed in this experiment would be useful inmodulating ABA, stress, and drought induced and/or regulated responses20000709 At_15mM_NH4NO3_L-to-H Promoters and cDNAs corresponding toendogenous cDNAs which were differentially expressed in this experimentwould be useful for modulating growth, yield and nitrogen inducedand/regulated responses 20000794 At_Petals Promoters and cDNAscorresponding to endogenous cDNAs which were differentially expressed inthis experiment would be useful for modulating fertility, fruit and seedsize, number and/or yield, including flowers development and number20001151 At_Line_Comparisons Promoters and cDNAs corresponding toendogenous cDNAs which were differentially expressed in this experimentwould be useful for modulating alkaloid biosynthesis and alkaloidinduced and/or regulated responses 20001184 At_Line_ComparisonsPromoters and cDNAs corresponding to endogenous cDNAs which weredifferentially expressed in this experiment would be useful formodulating methyl jasmonate induced and/or regulated responses includingbiosynthesis. They are useful also to modulate stress responses.20001195 At_Line_Comparisons Promoters and cDNAs corresponding toendogenous cDNAs which were differentially expressed in this experimentwould be useful for modulating alkaloid biosynthesis and alkaloidinduced and/or regulated responses 20001247 At_Far-red-inductionPromoters and cDNAs corresponding to endogenous cDNAs which weredifferentially expressed in this experiment would be useful formodulating shade avoidance 20001248 At_Far-red-induction Promoters andcDNAs corresponding to endogenous cDNAs which were differentiallyexpressed in this experiment would be useful for modulating shadeavoidance 20001307 At_Line_Comparisons Promoters and cDNAs correspondingto endogenous cDNAs which were differentially expressed in thisexperiment would be useful for modulating alkaloid biosynthesis andalkaloid induced and/or regulated responses 20001308 At_Line_ComparisonsPromoters and cDNAs corresponding to endogenous cDNAs which weredifferentially expressed in this experiment would be useful formodulating alkaloid biosynthesis and alkaloid induced and/or regulatedresponses 20001309 At_Line_Comparisons Promoters and cDNAs correspondingto endogenous cDNAs which were differentially expressed in thisexperiment would be useful for modulating alkaloid biosynthesis andalkaloid induced and/or regulated responses 20001310 At_Line_ComparisonsPromoters and cDNAs corresponding to endogenous cDNAs which weredifferentially expressed in this experiment would be useful formodulating alkaloid biosynthesis and alkaloid induced and/or regulatedresponses 20001318 At_Line_Comparisons Promoters and cDNAs correspondingto endogenous cDNAs which were differentially expressed in thisexperiment would be useful for modulating alkaloid biosynthesis andalkaloid induced and/or regulated responses 20001319 At_Line_ComparisonsPromoters and cDNAs corresponding to endogenous cDNAs which weredifferentially expressed in this experiment would be useful formodulating alkaloid biosynthesis and alkaloid induced and/or regulatedresponses 20001347 At_Line_Comparisons Promoters and cDNAs correspondingto endogenous cDNAs which were differentially expressed in thisexperiment would be useful for modulating methyl jasmonate inducedand/or regulated responses including biosynthesis. They are useful alsoto modulate stress responses. 20001450 At_Far-red-induction Promotersand cDNAs corresponding to endogenous cDNAs which were differentiallyexpressed in this experiment would be useful for modulating shadeavoidance 20001451 At_Far-red-induction Promoters and cDNAscorresponding to endogenous cDNAs which were differentially expressed inthis experiment would be useful for modulating shade avoidance 20001458At_50mM_NH4NO3_L-to-H Promoters and cDNAs corresponding to endogenouscDNAs which were differentially expressed in this experiment would beuseful for modulating growth, yield and nitrogen induced and/regulatedresponses 20001504 At_Far-red-enriched Promoters and cDNAs correspondingto endogenous cDNAs which were differentially expressed in thisexperiment would be useful for modulating shade avoidance 20001554At_Drought_Soil_Dry Promoters and cDNAs corresponding to endogenouscDNAs which were differentially expressed in this experiment would beuseful for modulating stress and drought tolerance 20001555At_Drought_Soil_Dry Promoters and cDNAs corresponding to endogenouscDNAs which were differentially expressed in this experiment would beuseful for modulating stress and drought tolerance 20001556At_Drought_Soil_Dry Promoters and cDNAs corresponding to endogenouscDNAs which were differentially expressed in this experiment would beuseful for modulating stress and drought tolerance 20001557At_Drought_Soil_Dry Promoters and cDNAs corresponding to endogenouscDNAs which were differentially expressed in this experiment would beuseful for modulating stress and drought tolerance 20001558At_Drought_Soil_Dry Promoters and cDNAs corresponding to endogenouscDNAs which were differentially expressed in this experiment would beuseful for modulating stress and drought tolerance 20001559At_Drought_Soil_Dry Promoters and cDNAs corresponding to endogenouscDNAs which were differentially expressed in this experiment would beuseful for modulating stress and drought tolerance 20001560At_Drought_Soil_Dry Promoters and cDNAs corresponding to endogenouscDNAs which were differentially expressed in this experiment would beuseful for modulating stress and drought tolerance 20001653At_Interploidy_Crosses Promoters and cDNAs corresponding to endogenouscDNAs which were differentially expressed in this experiment would beuseful for modulating fertility, fruit and seed size, number and/oryield, including endosperm size and seed abortion 20001654At_Interploidy_Crosses Promoters and cDNAs corresponding to endogenouscDNAs which were differentially expressed in this experiment would beuseful for modulating fertility, fruit and seed size, number and/oryield, including endosperm size and seed abortion 20001704At_Interploidy_Crosses Promoters and cDNAs corresponding to endogenouscDNAs which were differentially expressed in this experiment would beuseful for modulating fertility, fruit and seed size, number and/oryield, including endosperm size and seed abortion 20001757At_50mM_NH4NO3_L-to-H Promoters and cDNAs corresponding to endogenouscDNAs which were differentially expressed in this experiment would beuseful for modulating growth, yield and nitrogen induced and/regulatedresponses 20001768 At_Far-red-enriched-adult Promoters and cDNAscorresponding to endogenous cDNAs which were differentially expressed inthis experiment would be useful for modulating shade avoidance 20001770At_Far-red-enriched-adult Promoters and cDNAs corresponding toendogenous cDNAs which were differentially expressed in this experimentwould be useful for modulating shade avoidance 20001771At_Far-red-enriched-adult Promoters and cDNAs corresponding toendogenous cDNAs which were differentially expressed in this experimentwould be useful for modulating shade avoidance 20001773At_Far-red-enriched-adult Promoters and cDNAs corresponding toendogenous cDNAs which were differentially expressed in this experimentwould be useful for modulating shade avoidance 20001853At_Interploidy_Crosses Promoters and cDNAs corresponding to endogenouscDNAs which were differentially expressed in this experiment would beuseful for modulating fertility, fruit and seed size, number and/oryield, including endosperm size and seed abortion 20001904At_Drought_Reproduction Promoters and cDNAs corresponding to endogenouscDNAs which were differentially expressed in this experiment would beuseful for modulating stress and drought tolerance 20001905At_Drought_Reproduction Promoters and cDNAs corresponding to endogenouscDNAs which were differentially expressed in this experiment would beuseful for modulating stress and drought tolerance 20001906At_Drought_Reproduction Promoters and cDNAs corresponding to endogenouscDNAs which were differentially expressed in this experiment would beuseful for modulating stress and drought tolerance 20001907At_Drought_Reproduction Promoters and cDNAs corresponding to endogenouscDNAs which were differentially expressed in this experiment would beuseful for modulating stress and drought tolerance 20001908At_Drought_Reproduction Promoters and cDNAs corresponding to endogenouscDNAs which were differentially expressed in this experiment would beuseful for modulating stress and drought tolerance 20001909At_Drought_Reproduction Promoters and cDNAs corresponding to endogenouscDNAs which were differentially expressed in this experiment would beuseful for modulating stress and drought tolerance 20001910At_Drought_Reproduction Promoters and cDNAs corresponding to endogenouscDNAs which were differentially expressed in this experiment would beuseful for modulating stress and drought tolerance 20001911At_Drought_Reproduction Promoters and cDNAs corresponding to endogenouscDNAs which were differentially expressed in this experiment would beuseful for modulating stress and drought tolerance 20002007At_Line_Comparisons Promoters and cDNAs corresponding to endogenouscDNAs which were differentially expressed in this experiment would beuseful for modulating sterol biosynthesis and sterol induced and/orregulated responses. 20002008 At_Line_Comparisons Promoters and cDNAscorresponding to endogenous cDNAs which were differentially expressed inthis experiment would be useful for modulating sterol biosynthesis andsterol induced and/or regulated responses. 20002009 At_Line_ComparisonsPromoters and cDNAs corresponding to endogenous cDNAs which weredifferentially expressed in this experiment would be useful formodulating sterol biosynthesis and sterol induced and/or regulatedresponses. 20002010 At_Line_Comparisons Promoters and cDNAscorresponding to endogenous cDNAs which were differentially expressed inthis experiment would be useful for modulating sterol biosynthesis andsterol induced and/or regulated responses. 20002012 At_Line_ComparisonsPromoters and cDNAs corresponding to endogenous cDNAs which weredifferentially expressed in this experiment would be useful formodulating triterpene biosynthesis and triterpene induced and/orregulated responses. 20002103 At_8deg_Cold Promoters and cDNAscorresponding to endogenous cDNAs which were differentially expressed inthis experiment would be useful in modulating stress, heat and coldinduced and/or regulated responses 20002107 At_8deg_Cold Promoters andcDNAs corresponding to endogenous cDNAs which were differentiallyexpressed in this experiment would be useful in modulating stress, heatand cold induced and/or regulated responses

TABLE 3 Promoter Name Fl Si Lf St Em Ov Hy Co Rt YP0226 Y Y Y Y Y YP0244Y YP0286 Y Y Y Y Y YP0289 Y Y Y Y YP0356 Y Y Y Y Y Y YP0374 Y Y Y YP0377Y Y Y Y YP0380 Y Y Y Y Y Y Y YP0381 Y Y Y YP0382 Y Y YP0388 Y Y Y Y YYP0396 Y Y Y Y Y PT0506 Y PT0511 Y Y Y YP0275 Y YP0337 Y YP0384 Y YP0385Y Y Y YP0371 Y Y Legend for Table 3 Fl Flower Si Silique Lf Leaf St StemEm Embryo Ov Ovule Hy Hypocotyl Co Cotyledon Rt Rosette Leaf

The invention being thus described, it will be apparent to one ofordinary skill in the art that various modifications of the materialsand methods for practicing the invention can be made. Such modificationsare to be considered within the scope of the invention as defined by thefollowing claims.

Each of the references from the patent and periodical literature citedherein is hereby expressly incorporated in its entirety by suchcitation.

1. An isolated nucleic acid molecule having promoter activity consistingof a nucleotide sequence selected from the group consisting of: (a) anucleotide sequence according to SEQ ID NO:19; (b) a nucleotide sequenceconsisting of a functional fragment of (a), wherein said fragment haspromoter activity; and (c) a nucleotide sequence having at least 99%sequence identity to one of (a) or (b).
 2. A vector constructcomprising: a. a first nucleic acid selected from the group consistingof i. a nucleotide sequence according to SEQ ID NO:19, ii. a nucleotidesequence comprising a functional fragment of (i), wherein said fragmenthas promoter activity; and iii. a nucleotide sequence having at least99% sequence identity to one of (i) or (ii); and b. a second nucleicacid to be transcribed, wherein said first and second nucleic acidmolecules are heterologous to each other and are operably linkedtogether.
 3. A host cell comprising an isolated nucleic acid moleculeselected from the group consisting of (a) a nucleotide sequenceaccording to SEQ ID NO:19; (b) a nucleotide sequence comprising afunctional fragment of (a), wherein said fragment has promoter activity;and (c) a nucleotide sequence having at least 99% sequence identity toone of (a) or (b), wherein said nucleic acid molecule is flanked byexogenous sequence.
 4. A host cell comprising a vector construct ofclaim
 2. 5. A method of directing transcription in an environmentsuitable for transcription comprising: a. introducing a first nucleicacid molecule selected from the group consisting of i. a nucleotidesequence according to SEQ ID NO: 19, ii. a nucleotide sequencecomprising a functional fragment of (i), wherein said fragment haspromoter activity; and iii. a nucleotide sequence having at least 99%sequence identity to one of (i) or (ii) according to claim 1; and b.introducing a second nucleic acid molecule to be transcribed; whereinthe first and second nucleic acid molecules are heterologous to eachother and operably linked together, and wherein the second nucleic acidsequence is transcribed.
 6. A plant comprising a vector constructaccording to claim
 2. 7. The isolated nucleic acid of claim 1, whereinthe promoter activity occurs in response to drought.
 8. The isolatednucleic acid of claim 1, wherein said nucleotide sequence is SEQ IDNO:19 or a functional fragment thereof.
 9. The vector construct of claim6, wherein said nucleotide sequence is SEQ ID NO:19 or a functionalfragment thereof.
 10. The method of claim 5, wherein said nucleotidesequence is SEQ ID NO:19 or a functional fragment thereof.
 11. The plantof claim 6, wherein said nucleotide sequence is SEQ ID NO:19 or afunctional fragment thereof.
 12. The isolated nucleic acid of claim 1,wherein said nucleotide sequence is a functional fragment of SEQ IDNO:19.